PDB-4ghk: X-ray Crystal Structure of Gamma-glutamyl phosphate reductase fro...

ID or keywords:

Entry

Database: PDB / ID: 4ghk

Title

X-ray Crystal Structure of Gamma-glutamyl phosphate reductase from Burkholderia thailandensis

Components

Gamma-glutamyl phosphate reductase

Keywords

OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Gamma-glutamyl phosphate reductase

Function / homology

Function and homology information

glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / L-proline biosynthetic process / NADP binding / cytoplasm
Similarity search - Function

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...

History

Deposition	Aug 7, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ghk.cif.gz	596.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ghk.ent.gz	494.3 KB	Display	PDB format
PDBx/mmJSON format	4ghk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ghk_validation.pdf.gz	458.2 KB	Display	wwPDB validaton report
Full document	4ghk_full_validation.pdf.gz	466 KB	Display
Data in XML	4ghk_validation.xml.gz	58.7 KB	Display
Data in CIF	4ghk_validation.cif.gz	84.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gh/4ghk ftp://data.pdbj.org/pub/pdb/validation_reports/gh/4ghk	HTTPS FTP

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Related structure data

Related structure data	3d63C 3dahC 3eizC 3ej2C 3ek2C 3ezoC 3f0fC 3ftpC 3gk0C 3gk3C 3gvfC 3gwaC 3gweC 3imlC 3sz8C 3t4cC 3tmlC 3tmqC 3txyC 3u7jC 3ue9C 3uk1C 3uk2C 3undC 3uptC 3urrC 3uw1C 3uw2C 3uw3C 3v2iC 3v7nC 3v8hC 3v9oC 3v9pC 3vavC 4ddoC 4dfeC 4dheC 4dhkC 4dutC 4dz4C 4e4tC 4efiC 4eg0C 4egjC 4ek2C 4eqyC 4ewgC 4exqC 4f2gC 4f32C 4f3nC 4f3yC 4f4hC 4f7dC 4fk8C 4fryC 4g1kC 4g67C 4h3yC 4h3zC 4h4gC 1olaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1o20-2 6qib-d 6eo1-d 5l6s-2 1rzm-1 6qd2-d 5l6s-1 4kqe-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: ButhA.01417.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (5) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (5)

Deposited unit

A: Gamma-glutamyl phosphate reductase

B: Gamma-glutamyl phosphate reductase

C: Gamma-glutamyl phosphate reductase

D: Gamma-glutamyl phosphate reductase

191 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

2

A: Gamma-glutamyl phosphate reductase

B: Gamma-glutamyl phosphate reductase

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

3

C: Gamma-glutamyl phosphate reductase

D: Gamma-glutamyl phosphate reductase

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

Unit cell

Length a, b, c (Å)	85.410, 142.460, 154.760
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Gamma-glutamyl phosphate reductase / GPR / Glutamate-5-semialdehyde dehydrogenase / Glutamyl-gamma-semialdehyde dehydrogenase / GSA dehydrogenase Mass: 47659.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: proA, BTH_I1214 / Production host: Escherichia coli (E. coli) References: UniProt: Q2SZ88, glutamate-5-semialdehyde dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Gamma-glutamyl phosphate reductase / GPR / Glutamate-5-semialdehyde dehydrogenase / Glutamyl-gamma-semialdehyde dehydrogenase / GSA dehydrogenase

Mass: 47659.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: proA, BTH_I1214 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q2SZ88, glutamate-5-semialdehyde dehydrogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.47 Å³/Da / Density % sol: 50.19 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40% PEG 300, 200 mM Calcium Acetate, 100 mM sodium cacodylate pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.25→50 Å / Num. all: 90232 / Num. obs: 90052 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 36.944 Å² / R_merge(I) obs: 0.093 / Net I/σ(I): 13.59

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.25-2.31		0.551	2.65	1	99.9
2.31-2.37		0.482	3.07	1	99.9
2.37-2.44		0.41	3.59	1	99.9
2.44-2.52		0.356	4.17	1	99.9
2.52-2.6		0.303	4.99	1	99.9
2.6-2.69		0.255	5.93	1	99.9
2.69-2.79		0.22	6.89	1	99.9
2.79-2.9		0.184	8.19	1	100
2.9-3.03		0.143	10.45	1	99.9
3.03-3.18		0.113	12.82	1	99.9
3.18-3.35		0.087	16.13	1	99.8
3.35-3.56		0.071	19.41	1	99.8
3.56-3.8		0.056	23.16	1	99.9
3.8-4.11		0.047	27.47	1	99.8
4.11-4.5		0.04	31.55	1	99.9
4.5-5.03		0.037	32.99	1	99.8
5.03-5.81		0.041	30.53	1	99.9
5.81-7.12		0.04	30.39	1	99.8
7.12-10.06		0.026	42.5	1	99.4
	10.06	0.023	45.03	1	96

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OLA

1ola

Resolution: 2.25→45.398 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 22.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2245	4512	5.01 %
R_work	0.1805	-	-
obs	0.1828	90030	99.82 %
all	-	90232	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.9917 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→45.398 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11552	0	0	658	12210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11693
X-RAY DIFFRACTION	f_angle_d	1.039	15884
X-RAY DIFFRACTION	f_dihedral_angle_d	12.753	4158
X-RAY DIFFRACTION	f_chiral_restr	0.063	1942
X-RAY DIFFRACTION	f_plane_restr	0.004	2083

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 (%)
2.2499-2.2755	0.2787	128	0.2159	2810	X-RAY DIFFRACTION	100
2.2755-2.3023	0.2991	156	0.2168	2842	X-RAY DIFFRACTION	100
2.3023-2.3304	0.2418	170	0.2179	2776	X-RAY DIFFRACTION	100
2.3304-2.3599	0.2734	155	0.217	2813	X-RAY DIFFRACTION	100
2.3599-2.3909	0.2656	188	0.2121	2786	X-RAY DIFFRACTION	100
2.3909-2.4237	0.2352	121	0.2063	2841	X-RAY DIFFRACTION	100
2.4237-2.4583	0.2806	162	0.2047	2802	X-RAY DIFFRACTION	100
2.4583-2.495	0.2712	144	0.2056	2844	X-RAY DIFFRACTION	100
2.495-2.534	0.2588	144	0.1972	2820	X-RAY DIFFRACTION	100
2.534-2.5755	0.2671	152	0.195	2808	X-RAY DIFFRACTION	100
2.5755-2.6199	0.2452	128	0.1904	2867	X-RAY DIFFRACTION	100
2.6199-2.6675	0.2817	156	0.1896	2840	X-RAY DIFFRACTION	100
2.6675-2.7188	0.2345	148	0.1936	2824	X-RAY DIFFRACTION	100
2.7188-2.7743	0.27	139	0.1905	2850	X-RAY DIFFRACTION	100
2.7743-2.8346	0.2289	155	0.1922	2802	X-RAY DIFFRACTION	100
2.8346-2.9006	0.2915	143	0.1894	2843	X-RAY DIFFRACTION	100
2.9006-2.9731	0.2157	164	0.1922	2840	X-RAY DIFFRACTION	100
2.9731-3.0535	0.2174	142	0.1896	2867	X-RAY DIFFRACTION	100
3.0535-3.1433	0.263	159	0.194	2804	X-RAY DIFFRACTION	100
3.1433-3.2447	0.2575	145	0.193	2868	X-RAY DIFFRACTION	100
3.2447-3.3607	0.2441	149	0.1843	2824	X-RAY DIFFRACTION	100
3.3607-3.4952	0.2464	170	0.1827	2864	X-RAY DIFFRACTION	100
3.4952-3.6542	0.2377	136	0.1759	2865	X-RAY DIFFRACTION	100
3.6542-3.8467	0.206	126	0.1659	2905	X-RAY DIFFRACTION	100
3.8467-4.0876	0.2066	141	0.1564	2876	X-RAY DIFFRACTION	100
4.0876-4.403	0.153	145	0.1445	2878	X-RAY DIFFRACTION	100
4.403-4.8456	0.1752	151	0.1419	2894	X-RAY DIFFRACTION	100
4.8456-5.5457	0.1846	169	0.1635	2918	X-RAY DIFFRACTION	100
5.5457-6.9829	0.2095	161	0.1933	2924	X-RAY DIFFRACTION	100
6.9829-45.4068	0.1828	165	0.1761	3023	X-RAY DIFFRACTION	98

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	8.1125	-0.5944	0.7282	1.3129	-0.7055	1.4749	0.0885	-0.5852	-0.9056	-0.1158	0.1705	0.57	0.1592	-0.246	-0.189	0.2597	-0.0779	-0.0823	0.1896	0.0709	0.482	22.1014	23.9522	38.3906
2	2.2615	-0.5481	0.5065	1.8631	-0.1023	1.7045	0.2276	0.6249	-0.4671	-0.5211	-0.1459	0.3502	0.2105	0.0043	-0.0802	0.3373	0.0502	-0.0928	0.3261	-0.0549	0.3076	25.612	27.2739	28.8296
3	4.9568	-1.7381	1.2363	6.6717	-1.4058	7.4999	-0.053	0.5917	0.5015	-0.5821	0.2664	0.4949	-0.1921	-0.5897	-0.2077	0.2726	-0.0525	-0.0874	0.3205	0.0495	0.3868	15.9536	39.975	30.7558
4	5.8867	-0.3561	-0.791	1.334	-0.0033	5.5591	-0.1284	0.2852	-0.234	-0.361	0.0517	0.2326	0.1924	-0.3586	0.0806	0.265	-0.01	-0.0492	0.2445	-0.0083	0.1763	32.7476	59.3409	9.3428
5	4.8547	0.3728	0.1409	6.4704	1.6286	4.0185	-0.0247	0.1655	-0.0208	-0.3615	-0.0593	0.6097	0.3255	-0.9236	0.1126	0.2981	-0.0561	-0.0985	0.4631	0.02	0.2675	22.877	59.3347	1.9435
6	0.1695	0.1224	-0.235	1.488	-1.4032	2.0786	-0.0093	0.0688	0.0043	-0.0296	0.0588	0.1594	-0.0622	-0.1444	-0.0714	0.1743	0.0111	-0.0181	0.217	-0.035	0.2286	32.4264	52.7637	26.4336
7	4.3217	-0.1211	-1.1304	2.6144	0.2532	2.7855	0.2566	0.0827	0.6359	0.0696	-0.1353	0.3789	-0.2662	-0.0672	-0.0863	0.2503	0.0133	0.0836	0.1172	0.0166	0.3548	23.3558	70.7646	42.5909
8	1.8996	-0.6998	-1.1265	1.5517	1.5046	2.9622	0.0009	-0.4189	0.1314	0.3313	-0.1007	0.2231	0.0665	-0.1563	0.0856	0.2664	-0.076	0.0493	0.2841	-0.0208	0.2461	25.1315	63.305	48.9387
9	6.0793	1.4322	-0.2432	3.7801	0.8461	2.6542	0.3492	-0.5151	0.0205	0.4024	-0.3819	0.6908	0.1302	-0.4227	-0.0032	0.2478	-0.0447	0.0609	0.3146	-0.0138	0.3199	15.1856	59.3811	42.9916
10	6.701	0.3213	-0.4298	1.0916	1.2791	4.0377	-0.0372	-0.2416	0.2814	0.5083	-0.0453	0.1337	-0.2679	-0.2123	0.1145	0.3865	-0.0286	0.0318	0.2314	0.0362	0.181	29.3058	32.6435	67.5553
11	3.379	-0.7348	0.7696	2.8239	0.276	6.5625	0.0039	-0.1103	0.3291	0.0081	0.1859	0.5234	-0.7562	-0.6338	-0.1458	0.4215	0.0551	0.1199	0.3522	0.0294	0.3905	17.8756	32.352	73.0077
12	0.2005	0.027	-0.0699	1.6801	-1.2836	1.5146	-0.0168	-0.0266	0.0229	0.2447	0.0856	0.1253	-0.0076	-0.16	-0.0796	0.2308	-0.0376	0.0037	0.2133	-0.0196	0.2225	30.6532	39.6635	50.5959
13	4.4724	-0.9169	1.0447	2.7536	-0.6136	2.4071	0.1155	0.3795	0.1436	-0.3286	-0.2161	-0.3592	0.1958	0.5101	0.0303	0.2493	0.0734	0.0581	0.4199	0.0614	0.1792	66.6649	41.2321	16.8558
14	0.8459	-0.3317	-0.2253	1.8111	0.8392	1.499	0.0198	0.1396	-0.1573	0.112	0.0354	-0.3867	0.3383	0.2922	-0.0517	0.2489	0.0699	-0.0289	0.2883	0.0112	0.2785	66.543	35.1142	22.7183
15	7.409	-1.7074	0.8077	8.4372	-1.2	8.228	0.1399	-0.4213	-0.6602	0.5056	-0.1267	-0.6847	0.5287	0.9265	-0.0079	0.2582	0.0384	-0.0784	0.3648	0.0187	0.3661	74.7854	38.9312	35.2071
16	5.229	-0.2809	0.0153	4.813	-0.9118	1.3329	-0.0271	0.181	-0.1814	-0.2586	-0.168	-0.841	0.0866	0.2818	0.2006	0.3004	-0.0377	-0.0248	0.1984	0.044	0.3661	60.3234	14.1648	56.3091
17	1.6414	0.4426	-0.4749	3.8607	-1.0268	2.1163	-0.1231	-0.143	-0.3105	0.335	-0.1239	-0.9508	-0.0111	0.529	0.2218	0.2723	-0.0076	-0.1297	0.2866	0.0561	0.4763	65.9492	22.6426	57.8345
18	0.2408	-0.0655	0.1158	1.3571	-1.101	1.2913	0.004	-0.0156	-0.0271	0.1736	-0.1112	-0.229	-0.004	0.101	0.1298	0.1562	-0.0184	-0.058	0.2034	-0.0029	0.1882	55.6569	37.0996	43.8701
19	1.4694	0.0728	0.4908	2.1745	0.0557	2.2773	-0.1817	-0.1276	0.3563	0.3514	-0.0418	-0.3191	-0.9531	0.3001	0.1253	0.5898	-0.1243	-0.136	0.2804	0.0527	0.2937	61.9469	55.2994	57.8471
20	3.2186	0.6465	0.9388	5.1369	-0.8752	0.6965	-0.6154	-0.3147	0.4188	0.4091	0.5885	-0.3413	-1.2885	0.3494	-0.153	0.8801	-0.2594	-0.2927	0.4032	-0.0014	0.378	68.197	57.3829	65.5517
21	5.4751	0.2947	1.7713	2.5581	1.3105	3.2671	0.115	0.0162	0.4796	0.4065	-0.3481	-0.6798	-0.812	1.096	0.2886	0.4097	-0.1862	-0.0542	0.5247	0.0628	0.4656	75.9843	53.1603	49.1415
22	5.4356	0.142	0.2569	6.5985	-1.0212	0.4553	-0.0343	-0.4397	0.312	0.3462	0.0263	-0.4242	-0.1685	0.1857	0.0225	0.2081	-0.0181	0.0233	0.2169	-0.0014	0.2249	60.0388	75.9835	24.6651
23	3.1801	-0.5993	-0.2524	6.5191	-0.4637	6.5468	0.0902	-0.1737	0.2523	0.2769	-0.3836	-1.9813	0.3223	0.7079	0.2251	0.2436	-0.0225	-0.0142	0.3039	0.0517	0.6198	71.3051	80.9071	22.8469
24	0.2159	0.3056	-0.0994	2.5313	-1.575	1.5991	-0.0085	-0.0359	-0.0623	-0.0148	-0.136	-0.3828	-0.0624	0.1835	0.1779	0.1481	0.0058	-0.0029	0.2208	0.0019	0.228	58.6025	57.6321	32.4311

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:34)
2	X-RAY DIFFRACTION	2	(chain A and resid 35:194)
3	X-RAY DIFFRACTION	3	(chain A and resid 195:225)
4	X-RAY DIFFRACTION	4	(chain A and resid 226:278)
5	X-RAY DIFFRACTION	5	(chain A and resid 279:323)
6	X-RAY DIFFRACTION	6	(chain A and resid 324:422)
7	X-RAY DIFFRACTION	7	(chain B and resid 2:48)
8	X-RAY DIFFRACTION	8	(chain B and resid 49:169)
9	X-RAY DIFFRACTION	9	(chain B and resid 170:226)
10	X-RAY DIFFRACTION	10	(chain B and resid 227:278)
11	X-RAY DIFFRACTION	11	(chain B and resid 279:322)
12	X-RAY DIFFRACTION	12	(chain B and resid 323:422)
13	X-RAY DIFFRACTION	13	(chain C and resid 3:43)
14	X-RAY DIFFRACTION	14	(chain C and resid 44:195)
15	X-RAY DIFFRACTION	15	(chain C and resid 196:225)
16	X-RAY DIFFRACTION	16	(chain C and resid 228:304)
17	X-RAY DIFFRACTION	17	(chain C and resid 305:346)
18	X-RAY DIFFRACTION	18	(chain C and resid 347:422)
19	X-RAY DIFFRACTION	19	(chain D and resid 3:147)
20	X-RAY DIFFRACTION	20	(chain D and resid 148:181)
21	X-RAY DIFFRACTION	21	(chain D and resid 182:226)
22	X-RAY DIFFRACTION	22	(chain D and resid 227:284)
23	X-RAY DIFFRACTION	23	(chain D and resid 285:323)
24	X-RAY DIFFRACTION	24	(chain D and resid 324:422)

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