PDB-4yb7: Adenosine triphosphate phosphoribosyltransferase from Campylobact...

ID or keywords:

Entry

Database: PDB / ID: 4yb7

Title

Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with ATP

Components

ATP phosphoribosyltransferase

Keywords

TRANSFERASE /

Phosphoribosyltransferase /

hexamer /

ATP

Function / homology

Function and homology information

ATP phosphoribosyltransferase /

ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Mittelstaedt, G. / Moggre, G.-J. / Parker, E.J.

Citation

Journal: Protein Sci. / Year: 2016
Title: Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail.
Authors: Mittelstadt, G. / Moggre, G.J. / Panjikar, S. / Nazmi, A.R. / Parker, E.J.

History

Deposition	Feb 18, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 5, 2018	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yb7.cif.gz	672.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4yb7.ent.gz	559.4 KB	Display	PDB format
PDBx/mmJSON format	4yb7.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/yb/4yb7 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4yb7	HTTPS FTP

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Related structure data

Related structure data	4yb5C 4yb6C C: citing same article (ref.)
Similar structure data	5lhu-1 5lht-1 3dkx-1 6487 6dps-7 1rc6-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

B: ATP phosphoribosyltransferase

C: ATP phosphoribosyltransferase

D: ATP phosphoribosyltransferase

E: ATP phosphoribosyltransferase

I: ATP phosphoribosyltransferase

K: ATP phosphoribosyltransferase

A: ATP phosphoribosyltransferase

F: ATP phosphoribosyltransferase

G: ATP phosphoribosyltransferase

H: ATP phosphoribosyltransferase

J: ATP phosphoribosyltransferase

L: ATP phosphoribosyltransferase

hetero molecules

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

1

B: ATP phosphoribosyltransferase

C: ATP phosphoribosyltransferase

D: ATP phosphoribosyltransferase

E: ATP phosphoribosyltransferase

I: ATP phosphoribosyltransferase

K: ATP phosphoribosyltransferase

hetero molecules

defined by author&software
206 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: ATP phosphoribosyltransferase

F: ATP phosphoribosyltransferase

G: ATP phosphoribosyltransferase

H: ATP phosphoribosyltransferase

J: ATP phosphoribosyltransferase

L: ATP phosphoribosyltransferase

hetero molecules

defined by author&software
206 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.667, 91.835, 154.903
Angle α, β, γ (deg.)	101.11, 95.21, 118.14
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	B	4 - 299
2	1	C	4 - 299
1	2	B	4 - 299
2	2	D	4 - 299
1	3	B	5 - 298
2	3	E	5 - 298
1	4	B	4 - 299
2	4	I	4 - 299
1	5	B	4 - 299
2	5	K	4 - 299
1	6	B	4 - 299
2	6	A	4 - 299
1	7	B	4 - 299
2	7	F	4 - 299
1	8	B	5 - 299
2	8	G	5 - 299
1	9	B	4 - 299
2	9	H	4 - 299
1	10	B	4 - 299
2	10	J	4 - 299
1	11	B	5 - 299
2	11	L	5 - 299
1	12	C	4 - 299
2	12	D	4 - 299
1	13	C	5 - 299
2	13	E	5 - 299
1	14	C	4 - 299
2	14	I	4 - 299
1	15	C	4 - 299
2	15	K	4 - 299
1	16	C	4 - 299
2	16	A	4 - 299
1	17	C	4 - 299
2	17	F	4 - 299
1	18	C	5 - 299
2	18	G	5 - 299
1	19	C	4 - 299
2	19	H	4 - 299
1	20	C	4 - 299
2	20	J	4 - 299
1	21	C	5 - 299
2	21	L	5 - 299
1	22	D	5 - 299
2	22	E	5 - 299
1	23	D	4 - 299
2	23	I	4 - 299
1	24	D	4 - 299
2	24	K	4 - 299
1	25	D	4 - 299
2	25	A	4 - 299
1	26	D	4 - 299
2	26	F	4 - 299
1	27	D	5 - 299
2	27	G	5 - 299
1	28	D	4 - 299
2	28	H	4 - 299
1	29	D	4 - 299
2	29	J	4 - 299
1	30	D	5 - 299
2	30	L	5 - 299
1	31	E	5 - 299
2	31	I	5 - 299
1	32	E	5 - 299
2	32	K	5 - 299
1	33	E	5 - 298
2	33	A	5 - 298
1	34	E	5 - 299
2	34	F	5 - 299
1	35	E	5 - 299
2	35	G	5 - 299
1	36	E	5 - 298
2	36	H	5 - 298
1	37	E	5 - 298
2	37	J	5 - 298
1	38	E	5 - 299
2	38	L	5 - 299
1	39	I	4 - 299
2	39	K	4 - 299
1	40	I	4 - 299
2	40	A	4 - 299
1	41	I	4 - 299
2	41	F	4 - 299
1	42	I	5 - 299
2	42	G	5 - 299
1	43	I	4 - 299
2	43	H	4 - 299
1	44	I	4 - 299
2	44	J	4 - 299
1	45	I	5 - 299
2	45	L	5 - 299
1	46	K	4 - 299
2	46	A	4 - 299
1	47	K	4 - 299
2	47	F	4 - 299
1	48	K	5 - 299
2	48	G	5 - 299
1	49	K	4 - 299
2	49	H	4 - 299
1	50	K	4 - 299
2	50	J	4 - 299
1	51	K	5 - 298
2	51	L	5 - 298
1	52	A	4 - 299
2	52	F	4 - 299
1	53	A	5 - 299
2	53	G	5 - 299
1	54	A	4 - 299
2	54	H	4 - 299
1	55	A	4 - 299
2	55	J	4 - 299
1	56	A	5 - 299
2	56	L	5 - 299
1	57	F	5 - 298
2	57	G	5 - 298
1	58	F	4 - 299
2	58	H	4 - 299
1	59	F	4 - 299
2	59	J	4 - 299
1	60	F	5 - 299
2	60	L	5 - 299
1	61	G	5 - 299
2	61	H	5 - 299
1	62	G	5 - 299
2	62	J	5 - 299
1	63	G	5 - 299
2	63	L	5 - 299
1	64	H	4 - 299
2	64	J	4 - 299
1	65	H	5 - 299
2	65	L	5 - 299
1	66	J	5 - 299
2	66	L	5 - 299

NCS ensembles :

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Protein , 1 types, 12 molecules BCDEIKAFGHJL

#1: Protein	ATP phosphoribosyltransferase / / ATP-PRTase Mass: 33741.254 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter) Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HSJ4, ATP phosphoribosyltransferase

#1: Protein

ATP phosphoribosyltransferase /

/ ATP-PRTase

Mass: 33741.254 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni (strain RM1221) (Campylobacter)
Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST17 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HSJ4,

ATP phosphoribosyltransferase

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Non-polymers , 5 types, 396 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#5: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.86 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Sodium Acetate, Magnesium Chloride, PEG4000, ATP / Temp details: temperature controlled incubator

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.959 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.959 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 212958 / % possible obs: 98.1 % / Redundancy: 3.9 % / R_merge(I) obs: 0.076 / Net I/σ(I): 2
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 4 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.924 / SU B: 7.032 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25429	10624	5 %	RANDOM
R_work	0.23135	-	-	-
obs	0.23248	202326	98.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.811 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.13 Å²	-0.72 Å²	0.25 Å²
2-	-	0.01 Å²	0.47 Å²
3-	-	-	1.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26180	0	418	365	26963

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	26943
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	26157
X-RAY DIFFRACTION	r_angle_refined_deg	1.471	2.018	36609
X-RAY DIFFRACTION	r_angle_other_deg	1.523	3	59915
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.322	5	3516
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.42	24.954	971
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.52	15	4656
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.553	15	145
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	4432
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	30097
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	5432
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	2.574	4.597	14116
X-RAY DIFFRACTION	r_mcbond_other	2.574	4.597	14114
X-RAY DIFFRACTION	r_mcangle_it	3.991	6.883	17614
X-RAY DIFFRACTION	r_mcangle_other	3.991	6.883	17615
X-RAY DIFFRACTION	r_scbond_it	2.996	4.788	12827
X-RAY DIFFRACTION	r_scbond_other	2.996	4.788	12828
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.684	7.093	18996
X-RAY DIFFRACTION	r_long_range_B_refined	6.61	35.097	28019
X-RAY DIFFRACTION	r_long_range_B_other	6.61	35.099	28020
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	B	16686	0.1
1	2	C	16686	0.1
2	1	B	16497	0.08
2	2	D	16497	0.08
3	1	B	16378	0.1
3	2	E	16378	0.1
4	1	B	16204	0.08
4	2	I	16204	0.08
5	1	B	15955	0.11
5	2	K	15955	0.11
6	1	B	16889	0.09
6	2	A	16889	0.09
7	1	B	16556	0.09
7	2	F	16556	0.09
8	1	B	16136	0.09
8	2	G	16136	0.09
9	1	B	16223	0.08
9	2	H	16223	0.08
10	1	B	16880	0.08
10	2	J	16880	0.08
11	1	B	15859	0.09
11	2	L	15859	0.09
12	1	C	16215	0.09
12	2	D	16215	0.09
13	1	C	16381	0.09
13	2	E	16381	0.09
14	1	C	16037	0.09
14	2	I	16037	0.09
15	1	C	16009	0.09
15	2	K	16009	0.09
16	1	C	16648	0.09
16	2	A	16648	0.09
17	1	C	16957	0.08
17	2	F	16957	0.08
18	1	C	16089	0.08
18	2	G	16089	0.08
19	1	C	16045	0.07
19	2	H	16045	0.07
20	1	C	16697	0.07
20	2	J	16697	0.07
21	1	C	15892	0.08
21	2	L	15892	0.08
22	1	D	16032	0.09
22	2	E	16032	0.09
23	1	D	16014	0.08
23	2	I	16014	0.08
24	1	D	15731	0.09
24	2	K	15731	0.09
25	1	D	16245	0.09
25	2	A	16245	0.09
26	1	D	15989	0.09
26	2	F	15989	0.09
27	1	D	16004	0.09
27	2	G	16004	0.09
28	1	D	15930	0.07
28	2	H	15930	0.07
29	1	D	16084	0.09
29	2	J	16084	0.09
30	1	D	15323	0.09
30	2	L	15323	0.09
31	1	E	16022	0.09
31	2	I	16022	0.09
32	1	E	16318	0.08
32	2	K	16318	0.08
33	1	E	16797	0.08
33	2	A	16797	0.08
34	1	E	16373	0.08
34	2	F	16373	0.08
35	1	E	15966	0.08
35	2	G	15966	0.08
36	1	E	15982	0.08
36	2	H	15982	0.08
37	1	E	16918	0.08
37	2	J	16918	0.08
38	1	E	15901	0.08
38	2	L	15901	0.08
39	1	I	15781	0.09
39	2	K	15781	0.09
40	1	I	16208	0.08
40	2	A	16208	0.08
41	1	I	16083	0.08
41	2	F	16083	0.08
42	1	I	15832	0.08
42	2	G	15832	0.08
43	1	I	15895	0.07
43	2	H	15895	0.07
44	1	I	16333	0.08
44	2	J	16333	0.08
45	1	I	15156	0.09
45	2	L	15156	0.09
46	1	K	16542	0.08
46	2	A	16542	0.08
47	1	K	15986	0.09
47	2	F	15986	0.09
48	1	K	15772	0.08
48	2	G	15772	0.08
49	1	K	15499	0.08
49	2	H	15499	0.08
50	1	K	16434	0.09
50	2	J	16434	0.09
51	1	K	15600	0.09
51	2	L	15600	0.09
52	1	A	16626	0.08
52	2	F	16626	0.08
53	1	A	16290	0.07
53	2	G	16290	0.07
54	1	A	16064	0.08
54	2	H	16064	0.08
55	1	A	17125	0.07
55	2	J	17125	0.07
56	1	A	15946	0.08
56	2	L	15946	0.08
57	1	F	16193	0.07
57	2	G	16193	0.07
58	1	F	16080	0.07
58	2	H	16080	0.07
59	1	F	16900	0.07
59	2	J	16900	0.07
60	1	F	15654	0.08
60	2	L	15654	0.08
61	1	G	15605	0.07
61	2	H	15605	0.07
62	1	G	16140	0.07
62	2	J	16140	0.07
63	1	G	15176	0.08
63	2	L	15176	0.08
64	1	H	16358	0.07
64	2	J	16358	0.07
65	1	H	15492	0.07
65	2	L	15492	0.07
66	1	J	16048	0.07
66	2	L	16048	0.07

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	731	-
R_work	0.353	14869	-
obs	-	-	97.28 %

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Protein , 1 types, 12 molecules BCDEIKAFGHJL

-
Non-polymers , 5 types, 396 molecules

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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-Basic information

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-Protein , 1 types, 12 molecules BCDEIKAFGHJL

-Non-polymers , 5 types, 396 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

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+About Yorodumi

-News

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

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Protein , 1 types, 12 molecules BCDEIKAFGHJL

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Non-polymers , 5 types, 396 molecules

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