PDB-3pef: Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geo...

ID or keywords:

Entry

Database: PDB / ID: 3pef

Title

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens in complex with NADP+

Components

6-phosphogluconate dehydrogenase, NAD-binding

Keywords

OXIDOREDUCTASE / gamma-hydroxybutyrate dehydrogenase / succinic semialdehyde reductase / Geobacter metallireducens / NADP+

Function / homology

Function and homology information

organic acid catabolic process / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function

Biological species

Geobacter metallireducens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.07 Å

Authors

Zhang, Y. / Garavito, R.M.

Citation

Journal: Biochimie / Year: 2014
Title: Structural characterization of a beta-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity.
Authors: Zhang, Y. / Zheng, Y. / Qin, L. / Wang, S. / Buchko, G.W. / Garavito, R.M.

History

Deposition	Oct 26, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2016	Group: Database references
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pef.cif.gz	856.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3pef.ent.gz	716.4 KB	Display	PDB format
PDBx/mmJSON format	3pef.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3pef_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	3pef_full_validation.pdf.gz	2.8 MB	Display
Data in XML	3pef_validation.xml.gz	111.2 KB	Display
Data in CIF	3pef_validation.cif.gz	136.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/3pef ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pef	HTTPS FTP

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Related structure data

Related structure data	3pduC C: citing same article (ref.)
Similar structure data	3q3c-1 3pdu-1 3obb-1 3wy9-d 3pdu-2 2i9p-d 6smy-d 2uyy-d 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	#127 - Jul 2010 Crystallins similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 6-phosphogluconate dehydrogenase, NAD-binding

B: 6-phosphogluconate dehydrogenase, NAD-binding

C: 6-phosphogluconate dehydrogenase, NAD-binding

D: 6-phosphogluconate dehydrogenase, NAD-binding

E: 6-phosphogluconate dehydrogenase, NAD-binding

F: 6-phosphogluconate dehydrogenase, NAD-binding

G: 6-phosphogluconate dehydrogenase, NAD-binding

H: 6-phosphogluconate dehydrogenase, NAD-binding

hetero molecules

247 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6-phosphogluconate dehydrogenase, NAD-binding

B: 6-phosphogluconate dehydrogenase, NAD-binding

C: 6-phosphogluconate dehydrogenase, NAD-binding

D: 6-phosphogluconate dehydrogenase, NAD-binding

hetero molecules

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

2

E: 6-phosphogluconate dehydrogenase, NAD-binding

F: 6-phosphogluconate dehydrogenase, NAD-binding

G: 6-phosphogluconate dehydrogenase, NAD-binding

H: 6-phosphogluconate dehydrogenase, NAD-binding

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.968, 79.141, 95.470
Angle α, β, γ (deg.)	82.15, 88.80, 87.66
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	6-phosphogluconate dehydrogenase, NAD-binding Mass: 29924.719 Da / Num. of mol.: 8 / Mutation: M1S, I285Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter metallireducens (bacteria) / Gene: Gmet_3011 / Plasmid: pLW01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q39R98

#1: Protein

6-phosphogluconate dehydrogenase, NAD-binding

Mass: 29924.719 Da / Num. of mol.: 8 / Mutation: M1S, I285Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Geobacter metallireducens (bacteria) / Gene: Gmet_3011 / Plasmid: pLW01 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q39R98

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Non-polymers , 5 types, 1020 molecules

#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 999 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG4000, 0.1 M Tris-Meleate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.07→43.16 Å / Num. all: 127010 / Num. obs: 123216 / % possible obs: 70 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
AMoRE		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.07→43.157 Å / SU ML: 0.29 / σ(F): 1.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2091	3749	3.04 %
R_work	0.1556	-	-
all	0.1573	127010	-
obs	0.1573	123216	91.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.241 Å² / k_sol: 0.346 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.4878 Å²	0.4433 Å²	0.59 Å²
2-	-	1.2239 Å²	1.4156 Å²
3-	-	-	0.2639 Å²

Refinement step

Cycle: LAST / Resolution: 2.07→43.157 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16651	0	465	999	18115

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	17452
X-RAY DIFFRACTION	f_angle_d	1.166	23534
X-RAY DIFFRACTION	f_dihedral_angle_d	21.647	6457
X-RAY DIFFRACTION	f_chiral_restr	0.072	2600
X-RAY DIFFRACTION	f_plane_restr	0.004	3038

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 (%)
2.07-2.144	0.2969	260	0.2054	8981	X-RAY DIFFRACTION	69
2.144-2.2298	0.2646	331	0.1807	10486	X-RAY DIFFRACTION	81
2.2298-2.3313	0.2344	338	0.1783	11426	X-RAY DIFFRACTION	88
2.3313-2.4542	0.267	352	0.1814	12048	X-RAY DIFFRACTION	92
2.4542-2.608	0.2441	391	0.1779	12472	X-RAY DIFFRACTION	96
2.608-2.8093	0.24	442	0.175	12776	X-RAY DIFFRACTION	98
2.8093-3.0919	0.2381	393	0.1704	12720	X-RAY DIFFRACTION	98
3.0919-3.5392	0.2286	408	0.1675	12844	X-RAY DIFFRACTION	99
3.5392-4.4582	0.1752	414	0.1228	12905	X-RAY DIFFRACTION	99
4.4582-43.1663	0.1524	420	0.1276	12809	X-RAY DIFFRACTION	99

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	0.817	-0.543	-0.1509	0.8123	-0.3105	0.5608	-0.1014	-0.1436	-0.3258	0.1319	-0.0029	0.132	0.1139	0.0781	0.0884	0.1749	0.0243	0.0191	0.1356	0.0255	0.1735	4.5813	7.931	30.8825
2	1.0874	0.2065	-0.4748	0.8525	-0.1628	1.2894	0.0098	-0.2333	0.0369	0.1312	-0.065	0.0138	-0.1422	0.2169	0.0401	0.1823	-0.0235	-0.0074	0.1712	-0.0109	0.1468	7.9017	20.3721	31.6006
3	0.318	0.1627	0.0984	0.1555	-0.1837	0.6803	0.0039	0.0095	0.0254	-0.0118	-0.0467	0.163	0.0499	0.0219	0.0408	0.1729	-0.015	-0.0357	0.1045	-0.0319	0.1859	13.6742	18.5877	4.0985
4	1.0336	-0.1084	-0.0831	0.2098	0.3656	0.6281	-0.0079	0.009	-0.0556	0.0066	0.0867	0.1187	-0.0008	-0.0376	-0.0552	0.1987	-0.0065	-0.0436	0.119	0.0157	0.2086	2.9055	21.0005	6.6981
5	0.2207	0.0763	0.0759	0.1486	0.0761	0.1595	0.2927	0.5694	-0.1606	-0.3073	-0.2378	0.0896	0.0738	-0.1365	-0.0593	0.3691	0.114	-0.0499	0.5543	0.0706	0.2409	-13.6713	38.8886	-38.4388
6	0.7335	0.0087	0.1233	0.721	-0.4044	1.2472	0.1244	0.2993	0.0634	-0.2025	-0.0929	0.0539	-0.0183	0.0587	-0.0463	0.2487	0.066	-0.0247	0.3351	0.104	0.219	-6.2876	41.4758	-27.8324
7	1	-0.1082	-0.0004	0.4666	-0.1876	0.6133	0.1516	0.2326	0.0723	-0.1214	-0.0588	0.0827	0.1287	0.0389	-0.0796	0.2257	0.0075	-0.045	0.2126	0.0375	0.1979	-5.0739	32.5615	-14.0586
8	1.9631	0.6157	-1.3481	1.0646	-1.0604	1.4298	0.2457	-0.2768	0.0705	0.1088	-0.1137	0.1061	-0.2256	0.3489	-0.1242	0.3485	0.029	0.0559	0.3527	-0.0219	0.2977	-11.8034	26.0265	-4.7936
9	1.5196	-0.0979	0.2728	1.1995	-0.1856	0.9083	0.1326	0.7562	-0.0085	-0.4286	-0.2318	-0.1542	0.221	0.4101	0.0783	0.3298	0.1124	0.0709	0.5648	-0.0137	0.1473	32.0229	20.3633	-23.3338
10	0.5571	-0.5746	0.1665	0.6011	-0.2555	0.6585	0.0317	0.1437	0.0499	-0.0463	-0.0531	-0.0188	-0.0767	0.1313	0.0235	0.1952	-0.0333	-0.0002	0.2138	-0.025	0.1778	18.2348	25.6859	1.253
11	0.6948	0.0391	-0.3344	0.6086	-0.2194	0.799	0.097	0.1458	0.1079	-0.056	-0.0966	-0.0005	-0.0253	0.1252	0.0051	0.1746	0.0076	0.0088	0.1821	-0.0022	0.1655	18.6013	28.5601	-4.3623
12	0.6956	0.0479	-0.7407	0.3421	0.4004	1.5389	0.1261	-0.1032	0.3733	0.1435	0.0378	-0.0363	-0.2148	0.3067	-0.1134	0.2942	-0.0543	0.0206	0.216	0.0092	0.2327	22.1546	37.8545	-1.7358
13	0.3703	0.1205	-0.2474	0.3392	0.1654	0.579	0.1797	-0.1275	0.2727	-0.0907	0.0502	0.1191	-0.4136	0.0414	-0.1795	0.2505	0.0017	0.056	0.1362	-0.0438	0.343	-13.5207	62.5451	20.9909
14	1.1116	-0.3907	-0.5571	0.7749	0.4453	1.1049	-0.0605	-0.1097	-0.0146	0.0571	0.115	0.1054	-0.0516	-0.0705	-0.0323	0.1793	0.0279	0.0484	0.1369	0.0573	0.2621	-17.7216	49.3974	20.7428
15	0.2802	-0.2606	-0.158	0.2483	0.0142	0.7346	0.0143	0.0412	0.1776	0.0133	0.0473	-0.0144	-0.1128	-0.0288	-0.0593	0.1838	-0.0229	0.0207	0.1095	0.0445	0.2697	-3.3501	49.0291	-2.9252
16	0.5712	-0.1349	0.3764	0.5848	-0.4271	0.4464	0.0423	0.0951	0.17	0.1241	0.0266	0.0696	0.0011	0.0765	-0.0739	0.1777	-0.0233	0.0236	0.1421	0.0334	0.2685	2.1545	43.487	3.5572
17	1.167	0.2125	0.708	0.4811	-0.048	1.3584	-0.0602	0.1983	0.1889	-0.062	0.0256	0.1899	-0.0492	0.1272	0.0436	0.1719	-0.0226	-0.0205	0.1809	0.0202	0.2478	-34.6586	85.8275	-84.5795
18	0.6924	-0.1005	0.5575	0.2324	0.0666	1.254	0.05	0.1304	0.0944	0.0197	-0.0314	0.0435	0.1741	0.2753	-0.0379	0.1687	0.0245	0.0065	0.1734	-0.0364	0.1622	-24.7308	77.8478	-72.6078
19	0.7432	-0.1896	0.1078	0.1157	-0.1785	0.3286	-0.019	-0.076	-0.0021	0.1072	0.0573	-0.0096	0.0391	-0.021	-0.0379	0.1785	-0.0013	0.008	0.1429	-0.0513	0.1863	-29.6791	77.4559	-58.9468
20	1.0524	0.0774	-0.7885	1.1715	-0.2981	1.106	0.323	-0.299	0.1069	-0.0634	-0.0201	0.4162	-0.2759	0.0913	-0.2369	0.189	0.0186	0.0286	0.2158	-0.0636	0.3408	-37.3066	82.9802	-55.0427
21	0.8507	-0.4382	-0.2326	0.5962	0.1059	0.0985	-0.1606	-0.9621	0.0352	0.539	0.2584	0.0572	-0.293	-0.3837	-0.1308	0.447	0.1473	0.1312	1.0011	0.0959	0.2186	-43.8507	61.9535	-11.3483
22	0.5225	-0.4661	0.3291	0.5081	-0.1081	0.5458	0.0164	-0.4017	-0.1241	0.1266	0.0703	0.1907	0.0348	-0.2272	-0.1248	0.2045	-0.0285	0.0545	0.482	0.1195	0.2409	-41.9088	54.0665	-28.8965
23	0.1319	-0.0105	0.2719	0.8645	0.1858	1.0081	0.1144	-0.3878	-0.0544	0.1152	-0.0767	0.1919	-0.044	-0.1252	-0.0005	0.1813	0.0128	0.0793	0.3555	0.0341	0.2077	-42.8031	64.2436	-38.117
24	0.5744	-0.0652	0.7091	1.2727	-0.7791	1.2614	-0.0928	-0.0421	0.0942	-0.1309	0.2108	0.0808	-0.0011	-0.2342	-0.0056	0.3511	0.0083	0.0259	0.3921	-0.0235	0.3639	-48.4789	71.1971	-46.4526
25	0.6351	0.1839	0.1799	0.1794	-0.1249	0.3491	0.1125	-0.507	-0.0538	0.1726	-0.3207	-0.1563	-0.2	0.7405	0.2123	0.3122	-0.1076	-0.1181	0.8212	0.0967	0.255	3.6408	74.411	-31.865
26	1.2958	0.2568	-0.4005	0.5038	-0.0374	1.0513	0.1155	-0.6702	0.0212	0.1033	-0.1759	-0.0196	-0.1747	0.2628	0.0587	0.1981	-0.0823	-0.0206	0.5091	-0.0555	0.0896	-10.0925	77.8647	-34.5785
27	0.3612	0.1819	0.2364	0.3369	-0.0774	0.3011	0.0439	-0.2006	-0.0156	0.018	-0.1131	0.0306	0.0091	0.0148	0.0625	0.1877	0.0004	0.0079	0.2557	-0.007	0.1744	-17.9786	70.1874	-47.652
28	1.0728	-0.0751	0.0993	1.1308	-0.0712	1.1684	-0.1196	-0.4152	-0.0352	0.0002	0.2509	0.1381	-0.1133	0.0074	-0.0609	0.1634	0.0117	0.0249	0.2257	0.086	0.1696	-14.0266	60.7198	-50.8911
29	0.7455	0.0272	0.0225	0.1004	-0.1936	0.3814	0.0268	0.1417	-0.7092	-0.378	-0.0463	0.2679	0.4403	-0.0853	-0.0094	0.3424	-0.0842	-0.1122	0.1931	-0.0678	0.5879	-49.2552	35.3763	-72.2899
30	0.8052	-0.487	0.5639	0.6575	0.043	1.2605	0.1076	0.122	-0.2806	-0.2458	0.002	0.5011	0.1736	-0.2334	-0.107	0.2219	-0.0573	-0.1554	0.1988	-0.0155	0.4355	-54.1132	48.2101	-72.4421
31	0.282	0.2673	-0.0942	0.3336	-0.0242	0.5382	-0.013	-0.4015	-0.185	0.0496	0.0508	0.2142	0.0373	-0.2784	-0.0962	0.2143	0.0066	-0.0006	0.3033	0.076	0.3284	-41.4783	50.8848	-45.6958
32	0.8963	0.1661	-0.282	0.1094	-0.1412	0.6563	0.0059	-0.0967	-0.1557	-0.1091	-0.009	0.0598	0.0513	0.0269	-0.0009	0.1471	-0.0128	-0.0277	0.1392	0.0289	0.2608	-35.742	51.9893	-55.2335

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:43)
2	X-RAY DIFFRACTION	2	(chain A and resid 44:159)
3	X-RAY DIFFRACTION	3	(chain A and resid 160:221)
4	X-RAY DIFFRACTION	4	(chain A and resid 222:287)
5	X-RAY DIFFRACTION	5	(chain B and resid 1:34)
6	X-RAY DIFFRACTION	6	(chain B and resid 35:221)
7	X-RAY DIFFRACTION	7	(chain B and resid 222:282)
8	X-RAY DIFFRACTION	8	(chain B and resid 283:287)
9	X-RAY DIFFRACTION	9	(chain C and resid 1:162)
10	X-RAY DIFFRACTION	10	(chain C and resid 163:206)
11	X-RAY DIFFRACTION	11	(chain C and resid 207:268)
12	X-RAY DIFFRACTION	12	(chain C and resid 269:287)
13	X-RAY DIFFRACTION	13	(chain D and resid 1:45)
14	X-RAY DIFFRACTION	14	(chain D and resid 46:167)
15	X-RAY DIFFRACTION	15	(chain D and resid 168:248)
16	X-RAY DIFFRACTION	16	(chain D and resid 249:286)
17	X-RAY DIFFRACTION	17	(chain E and resid 1:82)
18	X-RAY DIFFRACTION	18	(chain E and resid 83:206)
19	X-RAY DIFFRACTION	19	(chain E and resid 207:268)
20	X-RAY DIFFRACTION	20	(chain E and resid 269:286)
21	X-RAY DIFFRACTION	21	(chain F and resid 2:93)
22	X-RAY DIFFRACTION	22	(chain F and resid 94:210)
23	X-RAY DIFFRACTION	23	(chain F and resid 211:281)
24	X-RAY DIFFRACTION	24	(chain F and resid 282:286)
25	X-RAY DIFFRACTION	25	(chain G and resid 1:42)
26	X-RAY DIFFRACTION	26	(chain G and resid 43:206)
27	X-RAY DIFFRACTION	27	(chain G and resid 207:268)
28	X-RAY DIFFRACTION	28	(chain G and resid 269:287)
29	X-RAY DIFFRACTION	29	(chain H and resid 2:45)
30	X-RAY DIFFRACTION	30	(chain H and resid 46:163)
31	X-RAY DIFFRACTION	31	(chain H and resid 164:217)
32	X-RAY DIFFRACTION	32	(chain H and resid 218:287)

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