PDB-6um4: Crystal structure of malate dehydrogenase from Naegleria fowleri ...

ID or keywords:

Entry

Database: PDB / ID: 6um4

Title

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID /

Structural Genomics /

Naegleria fowleri /

malate dehydrogenase / NF0021050 / Seattle Structural Genomics Center for Infectious Disease

Function / homology

L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain /

Alpha-Beta Complex /

Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Function and homology information

Biological species

Naegleria fowleri (brain-eating amoeba)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Oct 9, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6um4.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb6um4.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	6um4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/6um4 ftp://data.pdbj.org/pub/pdb/validation_reports/um/6um4	HTTPS FTP

-
Related structure data

Similar structure data	4psr-2 3d4p-2 6vdi-d 1y7t-d 3d0o-3 2ggs-d 4ni3-1 3d4p-3 1bdm-d 4psp-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

C: Malate dehydrogenase

D: Malate dehydrogenase

E: Malate dehydrogenase

F: Malate dehydrogenase

G: Malate dehydrogenase

H: Malate dehydrogenase

I: Malate dehydrogenase

J: Malate dehydrogenase

K: Malate dehydrogenase

L: Malate dehydrogenase

hetero molecules

587 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Malate dehydrogenase

B: Malate dehydrogenase

defined by author&software
Evidence: gel filtration
97.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Malate dehydrogenase

D: Malate dehydrogenase

hetero molecules

defined by author&software
97.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Malate dehydrogenase

F: Malate dehydrogenase

defined by author&software
97.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Malate dehydrogenase

H: Malate dehydrogenase

defined by author&software
97.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Malate dehydrogenase

J: Malate dehydrogenase

hetero molecules

defined by author&software
98 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Malate dehydrogenase

L: Malate dehydrogenase

hetero molecules

defined by author&software
97.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.330, 137.480, 139.280
Angle α, β, γ (deg.)	91.093, 89.998, 91.482
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1
10	1
11	1
12	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	GLY	GLY	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	94 - 104	94 - 104
1	2	GLY	GLY	LEU	LEU	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	107 - 158	107 - 158
1	3	GLU	GLU	SER	SER	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	160 - 166	160 - 166
1	4	ASN	ASN	PHE	PHE	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	168 - 171	168 - 171
1	5	GLY	GLY	PRO	PRO	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	173 - 184	173 - 184
1	6	MET	MET	LEU	LEU	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	189 - 220	189 - 220
1	7	VAL	VAL	THR	THR	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	222 - 292	222 - 292
1	8	LYS	LYS	ASP	ASP	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	294 - 304	294 - 304
1	9	GLN	GLN	ASP	ASP	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	306 - 398	306 - 398
1	10	ILE	ILE	ILE	ILE	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	400 - 408	400 - 408
1	11	GLU	GLU	VAL	VAL	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	410 - 414	410 - 414
1	12	ASN	ASN	LEU	LEU	(chain 'A' and (resid 94 through 105 or resid 107...	A	A	416 - 417	416 - 417
2	1	LEU	LEU	GLY	GLY	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	94 - 104	94 - 104
2	2	GLY	GLY	LEU	LEU	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	107 - 158	107 - 158
2	3	GLU	GLU	SER	SER	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	160 - 166	160 - 166
2	4	ASN	ASN	PHE	PHE	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	168 - 171	168 - 171
2	5	GLY	GLY	PRO	PRO	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	173 - 184	173 - 184
2	6	MET	MET	LEU	LEU	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	189 - 220	189 - 220
2	7	VAL	VAL	THR	THR	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	222 - 292	222 - 292
2	8	LYS	LYS	ASP	ASP	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	294 - 304	294 - 304
2	9	GLN	GLN	ASP	ASP	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	306 - 398	306 - 398
2	10	ILE	ILE	ILE	ILE	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	400 - 408	400 - 408
2	11	GLU	GLU	VAL	VAL	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	410 - 414	410 - 414
2	12	ASN	ASN	LEU	LEU	(chain 'B' and (resid 94 through 105 or resid 107...	B	B	416 - 417	416 - 417
3	1	LEU	LEU	GLY	GLY	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	94 - 104	94 - 104
3	2	GLY	GLY	LEU	LEU	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	107 - 158	107 - 158
3	3	GLU	GLU	SER	SER	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	160 - 166	160 - 166
3	4	ASN	ASN	PHE	PHE	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	168 - 171	168 - 171
3	5	GLY	GLY	PRO	PRO	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	173 - 184	173 - 184
3	6	MET	MET	LEU	LEU	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	189 - 220	189 - 220
3	7	VAL	VAL	THR	THR	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	222 - 292	222 - 292
3	8	LYS	LYS	ASP	ASP	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	294 - 304	294 - 304
3	9	GLN	GLN	ASP	ASP	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	306 - 398	306 - 398
3	10	ILE	ILE	ILE	ILE	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	400 - 408	400 - 408
3	11	GLU	GLU	VAL	VAL	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	410 - 414	410 - 414
3	12	ASN	ASN	LEU	LEU	(chain 'C' and (resid 94 through 105 or resid 107...	C	C	416 - 417	416 - 417
4	1	LEU	LEU	GLY	GLY	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	94 - 104	94 - 104
4	2	GLY	GLY	LEU	LEU	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	107 - 158	107 - 158
4	3	GLU	GLU	SER	SER	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	160 - 166	160 - 166
4	4	ASN	ASN	PHE	PHE	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	168 - 171	168 - 171
4	5	GLY	GLY	PRO	PRO	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	173 - 184	173 - 184
4	6	MET	MET	LEU	LEU	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	189 - 220	189 - 220
4	7	VAL	VAL	THR	THR	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	222 - 292	222 - 292
4	8	LYS	LYS	ASP	ASP	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	294 - 304	294 - 304
4	9	GLN	GLN	ASP	ASP	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	306 - 398	306 - 398
4	10	ILE	ILE	ILE	ILE	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	400 - 408	400 - 408
4	11	GLU	GLU	VAL	VAL	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	410 - 414	410 - 414
4	12	ASN	ASN	LEU	LEU	(chain 'D' and (resid 94 through 105 or resid 107...	D	D	416 - 417	416 - 417
5	1	LEU	LEU	GLY	GLY	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	94 - 104	94 - 104
5	2	GLY	GLY	LEU	LEU	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	107 - 158	107 - 158
5	3	GLU	GLU	SER	SER	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	160 - 166	160 - 166
5	4	ASN	ASN	PHE	PHE	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	168 - 171	168 - 171
5	5	GLY	GLY	PRO	PRO	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	173 - 184	173 - 184
5	6	MET	MET	LEU	LEU	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	189 - 220	189 - 220
5	7	VAL	VAL	THR	THR	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	222 - 292	222 - 292
5	8	LYS	LYS	ASP	ASP	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	294 - 304	294 - 304
5	9	GLN	GLN	ASP	ASP	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	306 - 398	306 - 398
5	10	ILE	ILE	ILE	ILE	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	400 - 408	400 - 408
5	11	GLU	GLU	VAL	VAL	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	410 - 414	410 - 414
5	12	ASN	ASN	LEU	LEU	(chain 'E' and (resid 94 through 105 or resid 107...	E	E	416 - 417	416 - 417
6	1	LEU	LEU	GLY	GLY	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	94 - 104	94 - 104
6	2	GLY	GLY	LEU	LEU	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	107 - 158	107 - 158
6	3	GLU	GLU	SER	SER	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	160 - 166	160 - 166
6	4	ASN	ASN	PHE	PHE	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	168 - 171	168 - 171
6	5	GLY	GLY	PRO	PRO	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	173 - 184	173 - 184
6	6	MET	MET	LEU	LEU	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	189 - 220	189 - 220
6	7	VAL	VAL	THR	THR	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	222 - 292	222 - 292
6	8	LYS	LYS	ASP	ASP	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	294 - 304	294 - 304
6	9	GLN	GLN	ASP	ASP	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	306 - 398	306 - 398
6	10	ILE	ILE	ILE	ILE	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	400 - 408	400 - 408
6	11	GLU	GLU	VAL	VAL	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	410 - 414	410 - 414
6	12	ASN	ASN	LEU	LEU	(chain 'F' and (resid 94 through 105 or resid 107...	F	F	416 - 417	416 - 417
7	1	LEU	LEU	GLY	GLY	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	94 - 104	94 - 104
7	2	GLY	GLY	LEU	LEU	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	107 - 158	107 - 158
7	3	GLU	GLU	SER	SER	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	160 - 166	160 - 166
7	4	ASN	ASN	PHE	PHE	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	168 - 171	168 - 171
7	5	GLY	GLY	PRO	PRO	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	173 - 184	173 - 184
7	6	MET	MET	LEU	LEU	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	189 - 220	189 - 220
7	7	VAL	VAL	THR	THR	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	222 - 292	222 - 292
7	8	LYS	LYS	ASP	ASP	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	294 - 304	294 - 304
7	9	GLN	GLN	ASP	ASP	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	306 - 398	306 - 398
7	10	ILE	ILE	ILE	ILE	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	400 - 408	400 - 408
7	11	GLU	GLU	VAL	VAL	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	410 - 414	410 - 414
7	12	ASN	ASN	LEU	LEU	(chain 'G' and (resid 94 through 105 or resid 107...	G	G	416 - 417	416 - 417
8	1	LEU	LEU	GLY	GLY	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	94 - 104	94 - 104
8	2	GLY	GLY	LEU	LEU	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	107 - 158	107 - 158
8	3	GLU	GLU	SER	SER	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	160 - 166	160 - 166
8	4	ASN	ASN	PHE	PHE	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	168 - 171	168 - 171
8	5	GLY	GLY	PRO	PRO	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	173 - 184	173 - 184
8	6	MET	MET	LEU	LEU	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	189 - 220	189 - 220
8	7	VAL	VAL	THR	THR	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	222 - 292	222 - 292
8	8	LYS	LYS	ASP	ASP	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	294 - 304	294 - 304
8	9	GLN	GLN	ASP	ASP	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	306 - 398	306 - 398
8	10	ILE	ILE	ILE	ILE	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	400 - 408	400 - 408
8	11	GLU	GLU	VAL	VAL	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	410 - 414	410 - 414
8	12	ASN	ASN	LEU	LEU	(chain 'H' and (resid 94 through 105 or resid 107...	H	H	416 - 417	416 - 417
9	1	LEU	LEU	GLY	GLY	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	94 - 104	94 - 104
9	2	GLY	GLY	LEU	LEU	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	107 - 158	107 - 158
9	3	GLU	GLU	SER	SER	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	160 - 166	160 - 166
9	4	ASN	ASN	PHE	PHE	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	168 - 171	168 - 171
9	5	GLY	GLY	PRO	PRO	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	173 - 184	173 - 184
9	6	MET	MET	LEU	LEU	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	189 - 220	189 - 220
9	7	VAL	VAL	THR	THR	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	222 - 292	222 - 292
9	8	LYS	LYS	ASP	ASP	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	294 - 304	294 - 304
9	9	GLN	GLN	ASP	ASP	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	306 - 398	306 - 398
9	10	ILE	ILE	ILE	ILE	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	400 - 408	400 - 408
9	11	GLU	GLU	VAL	VAL	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	410 - 414	410 - 414
9	12	ASN	ASN	LEU	LEU	(chain 'I' and (resid 94 through 105 or resid 107...	I	I	416 - 417	416 - 417
10	1	LEU	LEU	GLY	GLY	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	94 - 104	94 - 104
10	2	GLY	GLY	LEU	LEU	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	107 - 158	107 - 158
10	3	GLU	GLU	SER	SER	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	160 - 166	160 - 166
10	4	ASN	ASN	PHE	PHE	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	168 - 171	168 - 171
10	5	GLY	GLY	PRO	PRO	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	173 - 184	173 - 184
10	6	MET	MET	LEU	LEU	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	189 - 220	189 - 220
10	7	VAL	VAL	THR	THR	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	222 - 292	222 - 292
10	8	LYS	LYS	ASP	ASP	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	294 - 304	294 - 304
10	9	GLN	GLN	ASP	ASP	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	306 - 398	306 - 398
10	10	ILE	ILE	ILE	ILE	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	400 - 408	400 - 408
10	11	GLU	GLU	VAL	VAL	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	410 - 414	410 - 414
10	12	ASN	ASN	LEU	LEU	(chain 'J' and (resid 94 through 105 or resid 107...	J	J	416 - 417	416 - 417
11	1	LEU	LEU	GLY	GLY	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	94 - 104	94 - 104
11	2	GLY	GLY	LEU	LEU	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	107 - 158	107 - 158
11	3	GLU	GLU	SER	SER	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	160 - 166	160 - 166
11	4	ASN	ASN	PHE	PHE	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	168 - 171	168 - 171
11	5	GLY	GLY	PRO	PRO	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	173 - 184	173 - 184
11	6	MET	MET	LEU	LEU	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	189 - 220	189 - 220
11	7	VAL	VAL	THR	THR	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	222 - 292	222 - 292
11	8	LYS	LYS	ASP	ASP	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	294 - 304	294 - 304
11	9	GLN	GLN	ASP	ASP	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	306 - 398	306 - 398
11	10	ILE	ILE	ILE	ILE	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	400 - 408	400 - 408
11	11	GLU	GLU	VAL	VAL	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	410 - 414	410 - 414
11	12	ASN	ASN	LEU	LEU	(chain 'K' and (resid 94 through 105 or resid 107...	K	K	416 - 417	416 - 417
12	1	LEU	LEU	GLY	GLY	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	94 - 104	94 - 104
12	2	GLY	GLY	LEU	LEU	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	107 - 158	107 - 158
12	3	GLU	GLU	SER	SER	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	160 - 166	160 - 166
12	4	ASN	ASN	PHE	PHE	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	168 - 171	168 - 171
12	5	GLY	GLY	PRO	PRO	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	173 - 184	173 - 184
12	6	MET	MET	LEU	LEU	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	189 - 220	189 - 220
12	7	VAL	VAL	THR	THR	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	222 - 292	222 - 292
12	8	LYS	LYS	ASP	ASP	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	294 - 304	294 - 304
12	9	GLN	GLN	ASP	ASP	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	306 - 398	306 - 398
12	10	ILE	ILE	ILE	ILE	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	400 - 408	400 - 408
12	11	GLU	GLU	VAL	VAL	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	410 - 414	410 - 414
12	12	ASN	ASN	LEU	LEU	(chain 'L' and (resid 94 through 105 or resid 107...	L	L	416 - 417	416 - 417

#1: Protein	Malate dehydrogenase / / NafoA.00005.a.B1 Mass: 48929.793 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Gene: mRNA1_NF0021050 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2237 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.6 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Microlytics MCSG1 screen, condition H11: 25% PEG 3350, 200mM NaCl, 100mM HEPES / NaOH pH 7.5: NafoA.00005.a.B1.PS38166 at 16.9mg/ml + 2mM NAD. Cryo: 15% EG: tray: 298888 h11: puck eqq6-5.

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 1, 2018

Radiation

Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.05→44.23 Å / Num. obs: 271476 / % possible obs: 96.7 % / Redundancy: 2.645 % / B_iso Wilson estimate: 23.36 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.085 / R_rim(I) all: 0.108 / Χ²: 0.998 / Net I/σ(I): 8.18 / Num. measured all: 718188 / Scaling rejects: 104

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.05-2.1	2.656	0.512	2.01	52953	20736	19937	0.869	0.65	96.1
2.1-2.16	2.65	0.407	2.44	51734	20265	19523	0.917	0.516	96.3
2.16-2.22	2.656	0.339	2.91	50550	19752	19032	0.936	0.429	96.4
2.22-2.29	2.655	0.304	3.23	48774	19051	18370	0.948	0.385	96.4
2.29-2.37	2.652	0.271	3.53	47456	18528	17895	0.956	0.343	96.6
2.37-2.45	2.652	0.216	4.29	45893	17897	17303	0.971	0.274	96.7
2.45-2.54	2.646	0.179	5.02	44291	17316	16736	0.979	0.227	96.7
2.54-2.65	2.651	0.166	5.41	42711	16644	16113	0.981	0.211	96.8
2.65-2.76	2.649	0.141	6.38	40974	15992	15466	0.984	0.179	96.7
2.76-2.9	2.645	0.117	7.47	38984	15240	14741	0.988	0.149	96.7
2.9-3.06	2.644	0.096	8.85	37216	14488	14078	0.991	0.122	97.2
3.06-3.24	2.643	0.072	11.21	35342	13745	13373	0.995	0.092	97.3
3.24-3.47	2.636	0.061	13.14	32977	12859	12512	0.995	0.077	97.3
3.47-3.74	2.63	0.047	16.36	30758	12038	11694	0.997	0.059	97.1
3.74-4.1	2.636	0.041	17.74	28301	11048	10735	0.997	0.052	97.2
4.1-4.58	2.642	0.035	19.73	25471	9956	9640	0.998	0.044	96.8
4.58-5.29	2.64	0.034	19.72	22512	8773	8528	0.998	0.043	97.2
5.29-6.48	2.632	0.036	18.53	19063	7435	7242	0.998	0.046	97.4
6.48-9.17	2.621	0.032	21.1	14636	5743	5584	0.998	0.04	97.2
9.17-44.23	2.553	0.028	23.4	7592	3147	2974	0.998	0.035	94.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
ARP/wARP		model building
BUCCANEER		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1bdm_A as per MorDa

Resolution: 2.05→44.23 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.3053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2324	1853	0.68 %	0
R_work	0.2106	268817	-	-
obs	0.2108	270670	96.45 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→44.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28960	0	16	2237	31213

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	29671
X-RAY DIFFRACTION	f_angle_d	0.8406	40416
X-RAY DIFFRACTION	f_chiral_restr	0.0543	4597
X-RAY DIFFRACTION	f_plane_restr	0.0059	5384
X-RAY DIFFRACTION	f_dihedral_angle_d	17.1479	10702

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.11	0.3818	123	0.3148	20541	X-RAY DIFFRACTION	95.81
2.11-2.17	0.3228	101	0.2908	20624	X-RAY DIFFRACTION	95.95
2.17-2.24	0.2934	107	0.2795	20625	X-RAY DIFFRACTION	96.05
2.24-2.32	0.2744	137	0.2688	20663	X-RAY DIFFRACTION	96.2
2.32-2.41	0.3212	115	0.2506	20758	X-RAY DIFFRACTION	96.46
2.41-2.52	0.2762	184	0.229	20531	X-RAY DIFFRACTION	96.16
2.52-2.65	0.2849	168	0.2234	20636	X-RAY DIFFRACTION	96.51
2.65-2.82	0.2533	150	0.2211	20665	X-RAY DIFFRACTION	96.61
2.82-3.04	0.263	153	0.2296	20840	X-RAY DIFFRACTION	96.89
3.04-3.34	0.263	113	0.2046	20860	X-RAY DIFFRACTION	97.17
3.34-3.83	0.1979	165	0.1833	20756	X-RAY DIFFRACTION	97.12
3.83-4.82	0.1669	139	0.1567	20738	X-RAY DIFFRACTION	96.77
4.82-44.23	0.1873	198	0.1726	20580	X-RAY DIFFRACTION	96.14

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.47199763062	0.297531194092	0.0780333535503	0.720884927507	0.0650980407532	1.52222506383	-0.0309778975797	0.0420276825108	0.0149331928728	-0.0643767642672	0.0143328637605	-0.0592873936939	0.0218860973164	0.149901161938	0.0173855080118	0.134505162072	0.05604606837	0.00134854583578	0.382981810118	0.0112124621716	0.150560449369	3.73305345568	138.756285829	147.746929987
2	1.12326535393	-0.00512455490802	0.20245692537	0.597551142174	-0.109552654634	1.88820887722	0.01727280693	-0.253623374508	0.0110136428255	0.110423853256	-0.0196993327329	0.0579510426672	-0.0393386812049	-0.238115463013	0.00575538189534	0.171292219593	0.0166251044372	-0.00868436075296	0.518516867709	0.00297240889957	0.176690337334	-12.7130499751	136.426445909	178.056930038
3	1.75983622843	0.0333987109939	0.151196356551	0.505502577267	0.122304335084	2.11722244868	-0.0123587024393	-0.0850322193973	0.0343682480431	-0.0442808630917	-0.0187236770194	-0.0576969463648	-0.0295318122639	0.0937598464181	0.0225726952	0.140199305181	0.0041871468645	0.0340976886064	0.292744650991	-0.0106242715939	0.189083776221	7.20501898995	92.3287975159	144.336015308
4	0.925125186315	0.127020047376	0.386452128021	0.525290544808	0.136752421624	2.01808232194	-0.00334853047262	-0.189315227865	0.0229138522419	0.116148599039	-0.0582715807923	0.0639877073684	0.0463520693175	-0.144745885817	0.0505944515006	0.173370746314	-0.00852398662225	0.0340425355952	0.482750536887	0.00769546238752	0.203769144558	-9.12254899887	91.3217288509	174.948888428
5	1.41810035667	0.0712478476376	-0.1627653635	0.488451470215	0.118524323417	2.25761792934	-0.0139824214253	-0.0864381679647	0.0485824244183	-0.0682536029409	-0.014743499377	-0.0221953025754	-0.0967445181571	0.125930498076	0.0119585070531	0.178752711122	0.0273725489328	0.0212816254612	0.42117640787	0.0133054454603	0.133890881982	5.98516520251	46.8714711233	146.063523574
6	1.28769099435	-0.0204478178003	0.242816403386	0.412170710159	-0.0344384047705	1.98787160107	0.00871792222455	-0.169355834988	0.0466871262552	0.0853143775693	-0.0315692086859	0.0389862606982	0.0384284484769	-0.113549601373	0.0140275404288	0.205631451418	0.00757414422923	0.0186682643754	0.569208726366	0.00706673613107	0.140156415447	-10.2374921502	45.2904059669	176.403277099
7	1.00701028547	0.076796922685	-0.205466822276	0.40764237103	-0.144113724012	2.10201444231	-0.0126520728853	0.118664230479	-0.0282563388623	-0.102014056836	0.000679346009608	0.0301443106104	-0.0380272939856	-0.0971092918413	0.0131721284945	0.202217778234	0.0816970378886	-0.00891422276611	0.571922485886	0.00220840232094	0.135809172593	16.3934660261	174.638378642	75.9984467916
8	1.50099018078	-0.0489845781033	0.0288386438969	0.5093355253	0.145643593492	2.05213403619	0.0179860206651	0.0459395661601	-0.0888887806836	0.0612863212546	-0.0147277695366	-0.0227208014812	0.115506480061	0.191609085991	-0.00844421012925	0.184283401062	0.0485396525828	-0.0128655166749	0.431399383029	0.0132852856455	0.131123761138	32.5232554268	172.988923182	106.526995107
9	1.36915192132	-0.0314756002268	-0.359006172604	0.38794711025	-0.00930271579649	1.81759111501	0.00563567643938	0.181798480642	-0.0640253552178	-0.087472842007	-0.0162126709255	0.0383006878856	-0.00583619077199	-0.11869302842	0.0248049197264	0.166888989236	0.0358899855468	-0.030112673542	0.525922283329	-0.0068780011928	0.19506708249	17.1958215109	128.617364848	77.9694698828
10	1.84022343922	-0.0100949070576	-0.265237959862	0.556339265741	0.165394390541	1.84493963758	-0.00999934353615	0.0550080742378	-0.0671655073994	0.0760838317096	-0.0118368794846	-0.0491320350663	-0.0095741071843	0.140157671528	0.0146569780966	0.161486625769	0.0140589719703	-0.0309001508696	0.391244938651	0.00396310938331	0.173333035156	33.7458518862	127.600496565	108.232107684
11	1.31556933728	-0.05867662398	-0.270745680223	0.667922120752	-0.0734378409229	2.01305866899	0.0112213342534	0.266201798037	0.0213063064831	-0.120785480317	-0.0462507794905	0.050777336049	-0.0306876497277	-0.287829519726	0.0136997959831	0.179514759852	0.00298568821959	0.0131535412387	0.461991309984	0.0153463701524	0.195179906962	21.1936878938	83.6203977785	74.550153158
12	1.62348426532	-0.213239946329	-0.0697477063693	0.842318952379	0.0603566510961	1.50768396114	-0.0362104287805	-0.114464871836	0.00580224851187	0.044623233922	-0.00392881938855	-0.0332556200874	0.00100539360706	0.122893937264	0.0267716065587	0.140957984415	-0.025194075913	-0.000627799336605	0.389877245763	-0.00297407894925	0.16160228999	37.402027805	81.1155255529	104.910363699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 93 through 501)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 93 through 418)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 93 through 418)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 94 through 501)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 93 through 418)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 93 through 418)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 93 through 418)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 93 through 418)
9	X-RAY DIFFRACTION	9	(chain 'I' and resid 93 through 418)
10	X-RAY DIFFRACTION	10	(chain 'J' and resid 93 through 501)
11	X-RAY DIFFRACTION	11	(chain 'K' and resid 93 through 418)
12	X-RAY DIFFRACTION	12	(chain 'L' and resid 93 through 501)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi