PDB-8juk: Crystal structure of Adenosine triphosphate phosphoribosyltransfe...

ID or keywords:

Entry

Database: PDB / ID: 8juk

Title

Crystal structure of Adenosine triphosphate phosphoribosyltransferase from Acinetobacter baumannii at 2.18 A resolution

Components

ATP phosphoribosyltransferase

Keywords

TRANSFERASE / HisG / ATPPRT / PRT / Histidine biosynthesis

Function / homology

Function and homology information

ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.181 Å

Authors

Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Adenosine triphosphate phosphoribosyltransferase from Acinetobacter baumannii at 2.18 A resolution
Authors: Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.

History

Deposition	Jun 26, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2023	Group: Data collection Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes Item: _pdbx_validate_planes.type

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8juk.cif.gz	109.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8juk.ent.gz	80.3 KB	Display	PDB format
PDBx/mmJSON format	8juk.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/ju/8juk ftp://data.pdbj.org/pub/pdb/validation_reports/ju/8juk	HTTPS FTP

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Related structure data

Similar structure data	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

Deposited unit

A: ATP phosphoribosyltransferase

B: ATP phosphoribosyltransferase

hetero molecules

50.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	71.476, 79.203, 97.777
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ATP phosphoribosyltransferase / ATP-PRT / ATP-PRTase Mass: 25113.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hisG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VGC6, ATP phosphoribosyltransferase
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.44 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: Sodium acetate trihydrate; Sodium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 1, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 2.18→97.78 Å / Num. obs: 29519 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC_1/2: 0.999 / Net I/σ(I): 14
Reflection shell	Resolution: 2.18→2.25 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2500 / CC_1/2: 0.74 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
MxCuBE		data collection
XDS		data reduction
Aimless		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.181→57.769 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.947 / SU B: 8.037 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R: 0.222 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2466	1499	5.087 %
R_work	0.1845	27966	-
all	0.188	-	-
obs	-	29465	99.564 %

Solvent computation

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

Displacement parameters

B_iso mean: 66.607 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.529 Å²	0 Å²	0 Å²
2-	-	3.233 Å²	-0 Å²
3-	-	-	-4.761 Å²

Refinement step

Cycle: LAST / Resolution: 2.181→57.769 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3518	0	10	248	3776

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	3572
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3621
X-RAY DIFFRACTION	r_angle_refined_deg	1.251	1.65	4822
X-RAY DIFFRACTION	r_angle_other_deg	0.4	1.573	8328
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.3	5	452
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.979	5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.204	10	678
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.383	10	148
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	573
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4126
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	750
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	651
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.208	0.2	3335
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1718
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2059
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.239	0.2	254
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.218	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.129	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.217	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	5.161	6.697	1815
X-RAY DIFFRACTION	r_mcbond_other	5.157	6.698	1815
X-RAY DIFFRACTION	r_mcangle_it	7.42	12.017	2264
X-RAY DIFFRACTION	r_mcangle_other	7.419	12.02	2265
X-RAY DIFFRACTION	r_scbond_it	6.279	7.463	1757
X-RAY DIFFRACTION	r_scbond_other	6.278	7.469	1758
X-RAY DIFFRACTION	r_scangle_it	9.454	13.382	2558
X-RAY DIFFRACTION	r_scangle_other	9.452	13.387	2559
X-RAY DIFFRACTION	r_lrange_it	13.048	80.87	14614
X-RAY DIFFRACTION	r_lrange_other	13.067	80.639	14388

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.181-2.238	0.347	130	0.327	1993	0.328	2151	0.894	0.894	98.6983	0.308
2.238-2.299	0.305	111	0.298	1972	0.298	2091	0.917	0.915	99.6174	0.275
2.299-2.365	0.323	113	0.282	1912	0.284	2037	0.914	0.932	99.4109	0.257
2.365-2.438	0.351	96	0.275	1877	0.279	1981	0.931	0.943	99.5962	0.252
2.438-2.518	0.35	92	0.266	1836	0.27	1937	0.9	0.948	99.5354	0.241
2.518-2.606	0.287	88	0.234	1752	0.237	1852	0.94	0.962	99.3521	0.208
2.606-2.704	0.301	74	0.22	1713	0.223	1797	0.931	0.969	99.4435	0.194
2.704-2.814	0.282	92	0.216	1654	0.219	1752	0.951	0.969	99.6575	0.19
2.814-2.939	0.272	75	0.213	1593	0.216	1672	0.948	0.97	99.7608	0.19
2.939-3.082	0.29	96	0.212	1490	0.217	1591	0.948	0.971	99.6857	0.196
3.082-3.249	0.251	89	0.203	1437	0.205	1530	0.956	0.973	99.7386	0.185
3.249-3.445	0.269	66	0.209	1394	0.212	1462	0.953	0.976	99.8632	0.2
3.445-3.682	0.278	62	0.186	1294	0.19	1357	0.953	0.981	99.9263	0.181
3.682-3.976	0.189	59	0.168	1224	0.169	1285	0.975	0.984	99.8444	0.165
3.976-4.353	0.236	56	0.156	1117	0.16	1174	0.968	0.984	99.9148	0.16
4.353-4.863	0.224	65	0.138	1013	0.144	1081	0.967	0.988	99.7225	0.147
4.863-5.609	0.27	48	0.163	906	0.168	955	0.962	0.986	99.8953	0.171
5.609-6.853	0.207	42	0.166	773	0.168	816	0.97	0.984	99.8775	0.175
6.853-9.625	0.172	29	0.128	635	0.13	666	0.98	0.99	99.6997	0.145
9.625-57.769	0.169	16	0.159	381	0.159	401	0.981	0.985	99.0025	0.2

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