PDB-4fmi: Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine

ID or keywords:

Entry

Database: PDB / ID: 4fmi

Title

Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine

Components

VP1

Keywords

VIRAL PROTEIN /

viral capsid protein / jelly roll / encapsidation /

receptor binding / sialylated oligosaccharides

Function / homology

Function and homology information

viral capsid / structural molecule activity
Similarity search - Function

Biological species

Merkel cell polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Neu, U. / Hengel, H. / Stehle, T.

Citation

Journal: Plos Pathog. / Year: 2012
Title: Structures of Merkel Cell Polyomavirus VP1 Complexes Define a Sialic Acid Binding Site Required for Infection.
Authors: Neu, U. / Hengel, H. / Blaum, B.S. / Schowalter, R.M. / Macejak, D. / Gilbert, M. / Wakarchuk, W.W. / Imamura, A. / Ando, H. / Kiso, M. / Arnberg, N. / Garcea, R.L. / Peters, T. / Buck, C.B. / Stehle, T.

History

Deposition	Jun 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fmi.cif.gz	2.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4fmi.ent.gz	1.8 MB	Display	PDB format
PDBx/mmJSON format	4fmi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fm/4fmi ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fmi	HTTPS FTP

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Related structure data

Related structure data	4fmgC 4fmhC 4fmjC C: citing same article (ref.)
Similar structure data	4fmh-1 4fmh-3 4u61-1 4fmj-3 6y67-3 4u61-2 3bwq-d 6hkv-1 4fmj-1 4fmh-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4fmgC

4fmhC

4fmjC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #113 - May 2009 Influenza Neuraminidase similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (4)

Deposited unit

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

643 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

hetero molecules

defined by author&software
160 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

defined by software
322 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

defined by software
321 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.040, 85.700, 248.730
Angle α, β, γ (deg.)	93.02, 100.41, 108.07
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	59 - 64
2	1	1	5	B	59 - 64
3	1	1	5	C	59 - 64
4	1	1	5	D	59 - 64
5	1	1	5	E	59 - 64
6	1	1	5	F	59 - 64
7	1	1	5	G	59 - 64
8	1	1	5	H	59 - 64
9	1	1	5	I	59 - 64
10	1	1	5	J	59 - 64
11	1	1	5	K	59 - 64
12	1	1	5	L	59 - 64
13	1	1	5	M	59 - 64
14	1	1	5	N	59 - 64
15	1	1	5	O	59 - 64
16	1	1	5	P	59 - 64
17	1	1	5	Q	59 - 64
18	1	1	5	R	59 - 64
19	1	1	5	S	59 - 64
20	1	1	5	T	59 - 64
1	2	1	5	A	96 - 100
2	2	1	5	B	96 - 100
3	2	1	5	C	96 - 100
4	2	1	5	D	96 - 100
5	2	1	5	E	96 - 100
6	2	1	5	F	96 - 100
7	2	1	5	G	96 - 100
8	2	1	5	H	96 - 100
9	2	1	5	I	96 - 100
10	2	1	5	J	96 - 100
11	2	1	5	K	96 - 100
12	2	1	5	L	96 - 100
13	2	1	5	M	96 - 100
14	2	1	5	N	96 - 100
15	2	1	5	O	96 - 100
16	2	1	5	P	96 - 100
17	2	1	5	Q	96 - 100
18	2	1	5	R	96 - 100
19	2	1	5	S	96 - 100
20	2	1	5	T	96 - 100
1	3	1	5	A	123 - 142
2	3	1	5	B	123 - 142
3	3	1	5	C	123 - 142
4	3	1	5	D	123 - 142
5	3	1	5	E	123 - 142
6	3	1	5	F	123 - 142
7	3	1	5	G	123 - 142
8	3	1	5	H	123 - 142
9	3	1	5	I	123 - 142
10	3	1	5	J	123 - 142
11	3	1	5	K	123 - 142
12	3	1	5	L	123 - 142
13	3	1	5	M	123 - 142
14	3	1	5	N	123 - 142
15	3	1	5	O	123 - 142
16	3	1	5	P	123 - 142
17	3	1	5	Q	123 - 142
18	3	1	5	R	123 - 142
19	3	1	5	S	123 - 142
20	3	1	5	T	123 - 142
1	4	1	5	A	167 - 182
2	4	1	5	B	167 - 182
3	4	1	5	C	167 - 182
4	4	1	5	D	167 - 182
5	4	1	5	E	167 - 182
6	4	1	5	F	167 - 182
7	4	1	5	G	167 - 182
8	4	1	5	H	167 - 182
9	4	1	5	I	167 - 182
10	4	1	5	J	167 - 182
11	4	1	5	K	167 - 182
12	4	1	5	L	167 - 182
13	4	1	5	M	167 - 182
14	4	1	5	N	167 - 182
15	4	1	5	O	167 - 182
16	4	1	5	P	167 - 182
17	4	1	5	Q	167 - 182
18	4	1	5	R	167 - 182
19	4	1	5	S	167 - 182
20	4	1	5	T	167 - 182
1	5	1	5	A	311 - 316
2	5	1	5	B	311 - 316
3	5	1	5	C	311 - 316
4	5	1	5	D	311 - 316
5	5	1	5	E	311 - 316
6	5	1	5	F	311 - 316
7	5	1	5	G	311 - 316
8	5	1	5	H	311 - 316
9	5	1	5	I	311 - 316
10	5	1	5	J	311 - 316
11	5	1	5	K	311 - 316
12	5	1	5	L	311 - 316
13	5	1	5	M	311 - 316
14	5	1	5	N	311 - 316
15	5	1	5	O	311 - 316
16	5	1	5	P	311 - 316
17	5	1	5	Q	311 - 316
18	5	1	5	R	311 - 316
19	5	1	5	S	311 - 316
20	5	1	5	T	311 - 316
1	6	1	5	A	303 - 307
2	6	1	5	B	303 - 307
3	6	1	5	C	303 - 307
4	6	1	5	D	303 - 307
5	6	1	5	E	303 - 307
6	6	1	5	F	303 - 307
7	6	1	5	G	303 - 307
8	6	1	5	H	303 - 307
9	6	1	5	I	303 - 307
10	6	1	5	J	303 - 307
11	6	1	5	K	303 - 307
12	6	1	5	L	303 - 307
13	6	1	5	M	303 - 307
14	6	1	5	N	303 - 307
15	6	1	5	O	303 - 307
16	6	1	5	P	303 - 307
17	6	1	5	Q	303 - 307
18	6	1	5	R	303 - 307
19	6	1	5	S	303 - 307
20	6	1	5	T	303 - 307
1	7	1	5	A	259 - 261
2	7	1	5	B	259 - 261
3	7	1	5	C	259 - 261
4	7	1	5	D	259 - 261
5	7	1	5	E	259 - 261
6	7	1	5	F	259 - 261
7	7	1	5	G	259 - 261
8	7	1	5	H	259 - 261
9	7	1	5	I	259 - 261
10	7	1	5	J	259 - 261
11	7	1	5	K	259 - 261
12	7	1	5	L	259 - 261
13	7	1	5	M	259 - 261
14	7	1	5	N	259 - 261
15	7	1	5	O	259 - 261
16	7	1	5	P	259 - 261
17	7	1	5	Q	259 - 261
18	7	1	5	R	259 - 261
19	7	1	5	S	259 - 261
20	7	1	5	T	259 - 261
1	8	1	5	A	272 - 275
2	8	1	5	B	272 - 275
3	8	1	5	C	272 - 275
4	8	1	5	D	272 - 275
5	8	1	5	E	272 - 275
6	8	1	5	F	272 - 275
7	8	1	5	G	272 - 275
8	8	1	5	H	272 - 275
9	8	1	5	I	272 - 275
10	8	1	5	J	272 - 275
11	8	1	5	K	272 - 275
12	8	1	5	L	272 - 275
13	8	1	5	M	272 - 275
14	8	1	5	N	272 - 275
15	8	1	5	O	272 - 275
16	8	1	5	P	272 - 275
17	8	1	5	Q	272 - 275
18	8	1	5	R	272 - 275
19	8	1	5	S	272 - 275
20	8	1	5	T	272 - 275
1	9	1	5	A	224 - 238
2	9	1	5	B	224 - 238
3	9	1	5	C	224 - 238
4	9	1	5	D	224 - 238
5	9	1	5	E	224 - 238
6	9	1	5	F	224 - 238
7	9	1	5	G	224 - 238
8	9	1	5	H	224 - 238
9	9	1	5	I	224 - 238
10	9	1	5	J	224 - 238
11	9	1	5	K	224 - 238
12	9	1	5	L	224 - 238
13	9	1	5	M	224 - 238
14	9	1	5	N	224 - 238
15	9	1	5	O	224 - 238
16	9	1	5	P	224 - 238
17	9	1	5	Q	224 - 238
18	9	1	5	R	224 - 238
19	9	1	5	S	224 - 238
20	9	1	5	T	224 - 238
1	10	1	5	A	243 - 248
2	10	1	5	B	243 - 248
3	10	1	5	C	243 - 248
4	10	1	5	D	243 - 248
5	10	1	5	E	243 - 248
6	10	1	5	F	243 - 248
7	10	1	5	G	243 - 248
8	10	1	5	H	243 - 248
9	10	1	5	I	243 - 248
10	10	1	5	J	243 - 248
11	10	1	5	K	243 - 248
12	10	1	5	L	243 - 248
13	10	1	5	M	243 - 248
14	10	1	5	N	243 - 248
15	10	1	5	O	243 - 248
16	10	1	5	P	243 - 248
17	10	1	5	Q	243 - 248
18	10	1	5	R	243 - 248
19	10	1	5	S	243 - 248
20	10	1	5	T	243 - 248
1	11	1	5	A	284 - 294
2	11	1	5	B	284 - 294
3	11	1	5	C	284 - 294
4	11	1	5	D	284 - 294
5	11	1	5	E	284 - 294
6	11	1	5	F	284 - 294
7	11	1	5	G	284 - 294
8	11	1	5	H	284 - 294
9	11	1	5	I	284 - 294
10	11	1	5	J	284 - 294
11	11	1	5	K	284 - 294
12	11	1	5	L	284 - 294
13	11	1	5	M	284 - 294
14	11	1	5	N	284 - 294
15	11	1	5	O	284 - 294
16	11	1	5	P	284 - 294
17	11	1	5	Q	284 - 294
18	11	1	5	R	284 - 294
19	11	1	5	S	284 - 294
20	11	1	5	T	284 - 294
1	12	1	5	A	153 - 156
2	12	1	5	B	153 - 156
3	12	1	5	C	153 - 156
4	12	1	5	D	153 - 156
5	12	1	5	E	153 - 156
6	12	1	5	F	153 - 156
7	12	1	5	G	153 - 156
8	12	1	5	H	153 - 156
9	12	1	5	I	153 - 156
10	12	1	5	J	153 - 156
11	12	1	5	K	153 - 156
12	12	1	5	L	153 - 156
13	12	1	5	M	153 - 156
14	12	1	5	N	153 - 156
15	12	1	5	O	153 - 156
16	12	1	5	P	153 - 156
17	12	1	5	Q	153 - 156
18	12	1	5	R	153 - 156
19	12	1	5	S	153 - 156
20	12	1	5	T	153 - 156
1	13	1	5	A	190 - 196
2	13	1	5	B	190 - 196
3	13	1	5	C	190 - 196
4	13	1	5	D	190 - 196
5	13	1	5	E	190 - 196
6	13	1	5	F	190 - 196
7	13	1	5	G	190 - 196
8	13	1	5	H	190 - 196
9	13	1	5	I	190 - 196
10	13	1	5	J	190 - 196
11	13	1	5	K	190 - 196
12	13	1	5	L	190 - 196
13	13	1	5	M	190 - 196
14	13	1	5	N	190 - 196
15	13	1	5	O	190 - 196
16	13	1	5	P	190 - 196
17	13	1	5	Q	190 - 196
18	13	1	5	R	190 - 196
19	13	1	5	S	190 - 196
20	13	1	5	T	190 - 196
1	14	1	5	A	254 - 257
2	14	1	5	B	254 - 257
3	14	1	5	C	254 - 257
4	14	1	5	D	254 - 257
5	14	1	5	E	254 - 257
6	14	1	5	F	254 - 257
7	14	1	5	G	254 - 257
8	14	1	5	H	254 - 257
9	14	1	5	I	254 - 257
10	14	1	5	J	254 - 257
11	14	1	5	K	254 - 257
12	14	1	5	L	254 - 257
13	14	1	5	M	254 - 257
14	14	1	5	N	254 - 257
15	14	1	5	O	254 - 257
16	14	1	5	P	254 - 257
17	14	1	5	Q	254 - 257
18	14	1	5	R	254 - 257
19	14	1	5	S	254 - 257
20	14	1	5	T	254 - 257
1	15	1	5	A	264 - 269
2	15	1	5	B	264 - 269
3	15	1	5	C	264 - 269
4	15	1	5	D	264 - 269
5	15	1	5	E	264 - 269
6	15	1	5	F	264 - 269
7	15	1	5	G	264 - 269
8	15	1	5	H	264 - 269
9	15	1	5	I	264 - 269
10	15	1	5	J	264 - 269
11	15	1	5	K	264 - 269
12	15	1	5	L	264 - 269
13	15	1	5	M	264 - 269
14	15	1	5	N	264 - 269
15	15	1	5	O	264 - 269
16	15	1	5	P	264 - 269
17	15	1	5	Q	264 - 269
18	15	1	5	R	264 - 269
19	15	1	5	S	264 - 269
20	15	1	5	T	264 - 269

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Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein	VP1 Mass: 31927.154 Da / Num. of mol.: 20 / Fragment: UNP residues 37-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Merkel cell polyomavirus / Strain: W162 / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: C0JPK1

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Sugars , 3 types, 4 molecules

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine

Type: oligosaccharide

, Oligosaccharide

/ Class: Substrate analog

/ Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5NCC/3=O]/1-2-3/a4-b1_b3-c2	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#3: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose

Type: oligosaccharide

/ Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2	WURCS	PDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}	LINUCS	PDB-CARE

#6: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid /

Sialic acid

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 3 types, 3723 molecules

#4: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	... ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3677 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.35 % Description: THE CRYSTAL SUFFERED FROM RADIATION DAMAGE DURING DATA COLLECTION.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate, pH 6.5, 6% w/v PEG3350, 0.3 M magnesium chloride, soaked in 20 mM 3'-sialyllactosamine, cryoprotection: 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2010
Radiation	Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 440784 / Num. obs: 395073 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / R_merge(I) obs: 0.085 / Net I/σ(I): 8.24
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 1.62

-
Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.915 / SU B: 8.948 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE BINDING SITES IN CHAINS B, C, H, J, K, O, Q, R AND S CONTAIN ONLY VERY WEAK ELECTRON DENSITY FEATURES FOR THE LIGAND. RESIDUES 71 AND 72 ADOPT MULTIPLE CONFORMATIONS IN THE STRUCTURE.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23589	3934	1 %	RANDOM
R_work	0.19559	-	-	-
obs	0.196	391137	89.65 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 23.911 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.54 Å²	-0.11 Å²	-0.63 Å²
2-	-	1.37 Å²	-0.21 Å²
3-	-	-	-1.16 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42708	0	291	3677	46676

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	44469
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.111	1.978	60666
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.031	5	5544
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.564	25.073	1839
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.442	15	7353
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.536	15	163
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	6827
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	33576
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.015	3	27593
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.785	5	45061
X-RAY DIFFRACTION	r_scbond_it	2.648	7	16876
X-RAY DIFFRACTION	r_scangle_it	3.866	9	15594
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	452	medium positional	0.08	0.5
2	B	452	medium positional	0.09	0.5
3	C	452	medium positional	0.1	0.5
4	D	452	medium positional	0.07	0.5
5	E	452	medium positional	0.09	0.5
6	F	452	medium positional	0.09	0.5
7	G	452	medium positional	0.08	0.5
8	H	452	medium positional	0.09	0.5
9	I	452	medium positional	0.1	0.5
10	J	452	medium positional	0.08	0.5
11	K	452	medium positional	0.09	0.5
12	L	452	medium positional	0.09	0.5
13	M	452	medium positional	0.09	0.5
14	N	452	medium positional	0.09	0.5
15	O	452	medium positional	0.09	0.5
16	P	452	medium positional	0.08	0.5
17	Q	452	medium positional	0.08	0.5
18	R	452	medium positional	0.08	0.5
19	S	452	medium positional	0.07	0.5
20	T	452	medium positional	0.08	0.5
1	A	403	loose positional	0.12	5
2	B	403	loose positional	0.14	5
3	C	403	loose positional	0.14	5
4	D	403	loose positional	0.13	5
5	E	403	loose positional	0.14	5
6	F	403	loose positional	0.13	5
7	G	403	loose positional	0.13	5
8	H	403	loose positional	0.14	5
9	I	403	loose positional	0.14	5
10	J	403	loose positional	0.13	5
11	K	403	loose positional	0.12	5
12	L	403	loose positional	0.14	5
13	M	403	loose positional	0.14	5
14	N	403	loose positional	0.14	5
15	O	403	loose positional	0.13	5
16	P	403	loose positional	0.18	5
17	Q	403	loose positional	0.14	5
18	R	403	loose positional	0.17	5
19	S	403	loose positional	0.14	5
20	T	403	loose positional	0.13	5
1	A	452	medium thermal	0.57	2
2	B	452	medium thermal	0.59	2
3	C	452	medium thermal	0.62	2
4	D	452	medium thermal	0.59	2
5	E	452	medium thermal	0.61	2
6	F	452	medium thermal	0.72	2
7	G	452	medium thermal	0.55	2
8	H	452	medium thermal	0.58	2
9	I	452	medium thermal	0.69	2
10	J	452	medium thermal	0.64	2
11	K	452	medium thermal	0.57	2
12	L	452	medium thermal	0.6	2
13	M	452	medium thermal	0.64	2
14	N	452	medium thermal	0.62	2
15	O	452	medium thermal	0.57	2
16	P	452	medium thermal	0.68	2
17	Q	452	medium thermal	0.68	2
18	R	452	medium thermal	0.71	2
19	S	452	medium thermal	0.63	2
20	T	452	medium thermal	0.55	2
1	A	403	loose thermal	0.68	10
2	B	403	loose thermal	0.68	10
3	C	403	loose thermal	0.68	10
4	D	403	loose thermal	0.71	10
5	E	403	loose thermal	0.73	10
6	F	403	loose thermal	0.79	10
7	G	403	loose thermal	0.67	10
8	H	403	loose thermal	0.68	10
9	I	403	loose thermal	0.73	10
10	J	403	loose thermal	0.68	10
11	K	403	loose thermal	0.69	10
12	L	403	loose thermal	0.75	10
13	M	403	loose thermal	0.75	10
14	N	403	loose thermal	0.67	10
15	O	403	loose thermal	0.73	10
16	P	403	loose thermal	0.75	10
17	Q	403	loose thermal	0.74	10
18	R	403	loose thermal	0.77	10
19	S	403	loose thermal	0.71	10
20	T	403	loose thermal	0.66	10

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	212	-
R_work	0.299	24866	-
obs	-	-	77.01 %

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	2.0006	-0.8461	1.8229	1.1207	-1.1811	4.2252	-0.0875	0.2107	0.1864	-0.0256	-0.1645	-0.1045	-0.1813	0.4259	0.2521	0.0674	-0.0519	0.0095	0.0842	0.0089	0.1128	20.824	22.772	-7.52
2	0.3683	-0.0488	0.0735	0.3858	0.066	0.4861	-0.0125	0.0149	0.0828	-0.0216	-0.0203	0.012	-0.1224	0.057	0.0329	0.0337	-0.0218	-0.0098	0.0352	0.0002	0.05	12.12	20.491	1.732
3	1.0573	-0.1268	1.2865	1.616	-1.8807	4.8591	0.063	0.1054	-0.0829	-0.2504	0.0115	-0.1058	0.4817	0.0262	-0.0746	0.1152	0.0534	0.0393	0.1192	-0.0332	0.1289	24.085	-12.295	-16.976
4	0.5339	0.1411	0.0781	0.4436	-0.047	0.6637	-0.0283	0.0847	0.0167	-0.0589	0.014	-0.0449	0.0135	0.1706	0.0144	0.0189	0.0163	0.0132	0.0847	0.0064	0.0419	23.157	-3.909	-8.05
5	1.6448	0.2207	-0.015	1.0796	-1.2562	7.3335	0.0063	0.0213	-0.1178	-0.1357	0.0743	0.0593	0.4209	-0.4413	-0.0805	0.1874	-0.0005	0.0057	0.0531	-0.0569	0.1888	-8.061	-27.596	-15.384
6	0.408	-0.0151	0.008	0.304	0.0061	0.4506	0.0135	0.0312	-0.0762	-0.0557	-0.005	-0.0363	0.1273	0.0374	-0.0085	0.0564	0.0137	0.0109	0.0079	0.0027	0.0501	1.931	-23.942	-6.616
7	0.5323	-0.183	1.1301	0.8156	0.5788	5.6007	-0.0762	0.018	0.0265	-0.0836	-0.0368	0.0937	-0.1673	-0.4778	0.1129	0.0411	-0.0321	-0.0028	0.1464	-0.0104	0.1261	-30.696	-3.504	0.366
8	0.333	0.0594	-0.0473	0.4364	-0.02	0.5331	0.0094	0.0153	-0.0369	-0.0334	-0.0412	0.0434	0.0737	-0.1238	0.0318	0.0162	-0.0115	0.0059	0.0351	-0.0085	0.031	-21.04	-10.754	3.425
9	8.9033	2.2684	6.7133	1.5562	1.235	11.1983	-0.4945	0.6326	0.3285	-0.2621	0.1504	0.002	-0.7398	0.4214	0.3442	0.1383	0.0137	-0.0417	0.0763	0.0047	0.1141	-20.305	29.677	-14.994
10	0.5708	0.0457	0.0933	0.3974	-0.005	0.468	-0.0313	-0.026	0.0763	0.0001	-0.022	0.0509	-0.0819	-0.0654	0.0532	0.017	0.0071	-0.0061	0.0203	-0.0217	0.03	-14.475	17.18	9.17
11	8.2	1.7607	6.5739	2.5234	2.79	6.2218	-0.4019	0.2324	0.3115	-0.3305	0.0501	0.1754	-0.575	0.1431	0.3517	0.2129	0.0114	-0.0653	0.1206	0.0179	0.0946	14.95	5.185	-137.934
12	0.6519	0.0354	0.1998	0.4553	-0.0157	0.533	-0.0669	-0.0293	0.0549	0.0617	0.01	0.0832	-0.1457	-0.1061	0.0568	0.0578	0.0324	-0.0044	0.0226	-0.0095	0.0233	21.092	-5.128	-113.05
13	2.0458	-1.028	2.4526	0.9324	-0.9899	5.5061	0.0035	0.3772	0.1449	-0.1417	-0.153	-0.0642	0.1449	0.3658	0.1495	0.0985	-0.0615	-0.0228	0.1304	0.0431	0.0696	53.355	0.245	-135.849
14	0.3599	-0.0353	0.1426	0.4473	-0.0026	0.6395	-0.0433	0.0404	0.0796	0.0285	-0.01	-0.02	-0.1586	0.0896	0.0533	0.0728	-0.0256	-0.0274	0.0424	0.0068	0.0388	48.379	-2.349	-120.31
15	0.8532	-1.1293	0.7839	8.7366	-6.3486	8.8934	-0.1067	0.0658	-0.2173	-0.5129	0.1817	-0.1145	0.5452	0.0438	-0.075	0.0844	-0.01	0.0556	0.1899	-0.0029	0.0973	54.11	-29.666	-155.674
16	0.5283	0.1315	0.0551	0.5008	-0.0562	0.6459	-0.0159	0.0745	-0.0154	-0.0165	0.0102	-0.0704	0.057	0.1978	0.0056	0.0326	0.0342	-0.001	0.0824	0.0017	0.0478	59.304	-28.483	-128.074
17	5.3364	0.6317	-4.7238	2.6376	-1.9598	15.7593	-0.1138	0.5399	0.1055	-0.2661	0.2176	0.1842	0.6394	-0.7672	-0.1038	0.0886	-0.0402	-0.0216	0.083	-0.0043	0.056	25.371	-47.775	-149.325
18	0.4451	-0.0053	0.0241	0.4859	0.0123	0.5454	0.0088	0.0385	-0.0617	-0.0084	0.0143	-0.0292	0.2088	0.0069	-0.023	0.0974	0.0111	0.0056	0.0099	0.0057	0.0393	37.393	-47.373	-124.178
19	0.4123	0.0873	0.565	1.1088	0.3618	5.0174	-0.0694	0.0629	0.0282	-0.1226	-0.009	0.1531	-0.3089	-0.4682	0.0783	0.0486	0.0243	-0.0017	0.203	0.0105	0.1701	3.572	-26.353	-126.22
20	0.4526	0.0387	0.0195	0.5159	-0.0512	0.6711	0.0066	-0.022	-0.0402	0.0115	-0.017	0.0857	0.092	-0.1604	0.0104	0.0303	-0.0086	0.0205	0.0529	0.008	0.0352	14.297	-33.25	-115.883
21	5.9507	2.3157	5.2596	4.111	3.4788	13.4818	0.2176	-0.4871	-0.1334	0.6112	-0.0359	-0.1416	0.7146	-0.6848	-0.1818	0.1131	-0.0015	0.0016	0.1028	0.0062	0.0626	-36.857	19.573	-31.054
22	0.3775	-0.0112	0.1456	0.4579	0.0517	0.5461	0.003	-0.0785	0.0603	0.0092	-0.0373	0.0392	-0.0972	-0.1723	0.0342	0.0336	0.0255	-0.0059	0.0588	-0.0176	0.0397	-38.537	28.213	-58.19
23	1.6715	-0.3583	-0.512	1.5598	1.6336	11.9991	-0.0115	-0.2176	-0.0896	0.1974	0.0849	-0.0985	0.6332	0.2561	-0.0734	0.1329	-0.0313	-0.0129	0.054	0.0167	0.1144	-31.08	-11.945	-43.534
24	0.4299	-0.0614	0.0314	0.3017	0.0731	0.5671	0.0033	-0.0344	-0.0391	-0.004	-0.0165	0.0591	0.0918	-0.1203	0.0132	0.0357	-0.0213	-0.0118	0.0369	-0.0108	0.034	-37.491	0.459	-65.629
25	5.4562	2.6384	-0.9861	5.2165	-5.4351	10.9731	0.2844	-0.643	-0.0874	0.3295	-0.7112	-0.3012	-0.1603	1.0353	0.4267	0.1599	0.014	-0.0611	0.1852	-0.0011	0.1218	2.165	-13.341	-51.275
26	0.3271	0.0033	0.0417	0.4711	-0.0001	0.4946	0.0121	0.0078	-0.07	-0.031	-0.018	-0.0478	0.1157	0.0247	0.006	0.061	0.0108	0.0034	0.0117	-0.0102	0.0342	-10.447	-6.147	-73.976
27	0.661	-0.9802	1.4226	1.9069	-1.8242	4.3146	-0.0771	-0.0304	0.037	0.1939	-0.0116	-0.1411	-0.2981	0.217	0.0888	0.0631	-0.056	0.0012	0.1338	0.0164	0.1492	13.025	22.482	-60.143
28	0.3784	0	0.0703	0.3613	-0.0343	0.6891	-0.0015	0.0102	-0.0072	-0.0369	-0.011	-0.0785	-0.0311	0.1384	0.0124	0.0428	-0.0159	0.0219	0.0487	0.0031	0.0515	5.23	17.819	-72.276
29	2.5441	-0.6442	2.0859	1.1677	-0.7425	3.6131	-0.117	-0.1422	0.088	0.1086	0.0432	-0.0074	-0.444	0.0339	0.0739	0.1488	-0.0127	0.0024	0.0292	-0.0285	0.0786	-16.559	44.643	-52.752
30	0.3963	-0.0123	0.03	0.469	-0.0098	0.5887	-0.003	-0.0494	0.0593	-0.0141	-0.0165	-0.0565	-0.1682	0.0713	0.0194	0.0699	-0.0144	0.0055	0.0182	-0.0006	0.027	-11.434	38.712	-62.761
31	0.5573	-0.3205	0.5637	0.7836	0.4546	6.7046	0.0633	-0.0785	-0.0633	0.0711	-0.0787	0.0586	0.5884	-0.0273	0.0155	0.092	-0.0711	0.0055	0.1347	0.0212	0.139	0.954	-38.78	-181.327
32	0.5884	-0.1075	-0.0578	0.3905	0.0746	0.5268	0.0124	-0.0603	-0.0518	0.0432	-0.0109	0.0516	0.067	-0.0994	-0.0015	0.0339	-0.0346	-0.0145	0.071	0.0033	0.0627	-1.941	-27.311	-185.165
33	1.2392	0.1788	-0.099	0.6172	-0.3809	2.7568	0.0383	0.0929	-0.0478	0.0286	-0.0833	-0.0755	0.2168	0.4503	0.045	0.0765	0.0154	-0.0062	0.0997	-0.0116	0.0737	33.01	-36.287	-194.912
34	0.4208	0.0557	0.042	0.4702	-0.0246	0.583	0.0292	-0.0378	-0.0958	0.0209	-0.0168	-0.0078	0.117	0.0232	-0.0124	0.0374	-0.0015	-0.0139	0.0382	-0.0046	0.0551	24.106	-34.875	-193.13
35	3.3309	-2.4787	1.8342	5.6875	-3.6755	5.422	-0.2496	-0.2695	0.226	0.518	0.1307	-0.2609	-0.431	0.0357	0.1188	0.0885	-0.0456	-0.0266	0.1963	-0.0232	0.1083	51.728	-9.935	-168.934
36	0.3962	0.0061	0.0507	0.3407	-0.0854	0.5965	0.0021	0.0175	0.0046	-0.0137	-0.01	-0.0634	0.0171	0.1131	0.008	0.0137	-0.0186	0.0088	0.0674	0.0047	0.0405	41.055	-10.699	-194.601
37	6.5622	-1.261	3.7857	2.3676	-1.7591	5.8375	-0.1953	-0.7796	0.2965	0.3359	0.0967	0.0036	-0.4191	-0.3063	0.0987	0.1423	-0.0405	0.0009	0.1287	-0.0464	0.0758	27.35	12.05	-158.645
38	0.3749	0.0388	-0.0889	0.3205	-0.0666	0.5293	-0.011	-0.0311	0.0733	0.0186	0.0022	-0.014	-0.1256	0.048	0.0087	0.0341	-0.0066	-0.0027	0.0113	0.008	0.0478	23.211	11.215	-187.107
39	4.8494	2.2192	5.8615	4.9105	3.5958	13.0356	0.1291	-0.2023	-0.1619	0.5731	0.0954	-0.2003	0.5259	-0.5539	-0.2246	0.0908	0.0078	0.0037	0.122	-0.0233	0.094	-1.747	-5.979	-154.568
40	0.4093	-0.0058	0.0558	0.4345	-0.0263	0.3919	0.0051	-0.0245	0.0905	0.0368	-0.0186	0.04	-0.0735	-0.1097	0.0135	0.0181	0.014	0.0027	0.05	0.0062	0.0536	-2.9	0.408	-181.427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 77
2	X-RAY DIFFRACTION	2	A	78 - 319
3	X-RAY DIFFRACTION	3	B	41 - 77
4	X-RAY DIFFRACTION	4	B	78 - 319
5	X-RAY DIFFRACTION	5	C	40 - 73
6	X-RAY DIFFRACTION	6	C	74 - 319
7	X-RAY DIFFRACTION	7	D	40 - 79
8	X-RAY DIFFRACTION	8	D	80 - 319
9	X-RAY DIFFRACTION	9	E	40 - 57
10	X-RAY DIFFRACTION	10	E	58 - 319
11	X-RAY DIFFRACTION	11	F	40 - 57
12	X-RAY DIFFRACTION	12	F	58 - 319
13	X-RAY DIFFRACTION	13	G	41 - 69
14	X-RAY DIFFRACTION	14	G	70 - 319
15	X-RAY DIFFRACTION	15	H	40 - 56
16	X-RAY DIFFRACTION	16	H	57 - 319
17	X-RAY DIFFRACTION	17	I	40 - 57
18	X-RAY DIFFRACTION	18	I	58 - 319
19	X-RAY DIFFRACTION	19	J	41 - 69
20	X-RAY DIFFRACTION	20	J	70 - 319
21	X-RAY DIFFRACTION	21	K	40 - 56
22	X-RAY DIFFRACTION	22	K	57 - 319
23	X-RAY DIFFRACTION	23	L	39 - 58
24	X-RAY DIFFRACTION	24	L	59 - 319
25	X-RAY DIFFRACTION	25	M	40 - 57
26	X-RAY DIFFRACTION	26	M	58 - 320
27	X-RAY DIFFRACTION	27	N	40 - 70
28	X-RAY DIFFRACTION	28	N	71 - 320
29	X-RAY DIFFRACTION	29	O	41 - 77
30	X-RAY DIFFRACTION	30	O	78 - 319
31	X-RAY DIFFRACTION	31	P	41 - 78
32	X-RAY DIFFRACTION	32	P	79 - 319
33	X-RAY DIFFRACTION	33	Q	41 - 86
34	X-RAY DIFFRACTION	34	Q	87 - 319
35	X-RAY DIFFRACTION	35	R	40 - 56
36	X-RAY DIFFRACTION	36	R	57 - 320
37	X-RAY DIFFRACTION	37	S	40 - 56
38	X-RAY DIFFRACTION	38	S	57 - 319
39	X-RAY DIFFRACTION	39	T	40 - 57
40	X-RAY DIFFRACTION	40	T	58 - 319

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