PDB-4eso: Crystal structure of a putative oxidoreductase protein from Sinor...

ID or keywords:

Entry

Database: PDB / ID: 4eso

Title

Crystal structure of a putative oxidoreductase protein from Sinorhizobium meliloti 1021 in complex with NADP

Components

Putative oxidoreductase

Keywords

OXIDOREDUCTASE / NADP / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC

Function / homology

Function and homology information

Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Sinorhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.906 Å

Authors

Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)

Citation

Journal: To be Published
Title: Crystal structure of a putative oxidoreductase protein from Sinorhizobium meliloti 1021 in complex with NADP
Authors: Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C.

History

Deposition	Apr 23, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 16, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eso.cif.gz	385.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4eso.ent.gz	330.7 KB	Display	PDB format
PDBx/mmJSON format	4eso.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/es/4eso ftp://data.pdbj.org/pub/pdb/validation_reports/es/4eso	HTTPS FTP

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Related structure data

Related structure data	3vc7
Similar structure data	6ihh-1 3pib-d 4bms-1 2a56-1 5exb-1 2p68-1 2x9n-d 3grp-d 4osp-d 3oid-d 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: NYSGRC-012068

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Putative oxidoreductase

B: Putative oxidoreductase

C: Putative oxidoreductase

D: Putative oxidoreductase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	62.960, 66.740, 70.540
Angle α, β, γ (deg.)	66.50, 78.30, 62.96
Int Tables number	1
Space group name H-M	P1

Details

unknown

#1: Protein	Putative oxidoreductase Mass: 26864.686 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02322, SMc01571 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRIL / References: UniProt: Q92N93, Oxidoreductases
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.25 Å³/Da / Density % sol: 45.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium Acetate, 0.1 M HEPES, 25 % PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9598 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2012
Radiation	Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9598 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 128645 / % possible obs: 92.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 %
Reflection shell	Resolution: 1.9→1.93 Å / % possible all: 92.2

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Processing

Software

Name	Version	Classification
CBASS		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-3000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.906→34.849 Å / SU ML: 0.24 / σ(F): 1.96 / Phase error: 30.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2343	3346	5.1 %
R_work	0.1925	-	-
all	0.2145	68908	-
obs	0.1946	65562	89.63 %

Solvent computation

Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 33.94 Å² / k_sol: 0.3 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.3863 Å²	9.7683 Å²	-1.6647 Å²
2-	-	8.325 Å²	-6.3707 Å²
3-	-	-	-7.9387 Å²

Refinement step

Cycle: LAST / Resolution: 1.906→34.849 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7285	0	204	431	7920

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7695
X-RAY DIFFRACTION	f_angle_d	1.239	10464
X-RAY DIFFRACTION	f_dihedral_angle_d	19.069	2810
X-RAY DIFFRACTION	f_chiral_restr	0.076	1219
X-RAY DIFFRACTION	f_plane_restr	0.005	1356

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 (%)
1.9061-1.9333	0.4905	21	0.4536	327	X-RAY DIFFRACTION	12
1.9333-1.9622	0.4411	52	0.3906	1176	X-RAY DIFFRACTION	40
1.9622-1.9929	0.3663	116	0.3157	2194	X-RAY DIFFRACTION	76
1.9929-2.0255	0.343	137	0.2887	2745	X-RAY DIFFRACTION	95
2.0255-2.0604	0.364	129	0.2706	2729	X-RAY DIFFRACTION	95
2.0604-2.0979	0.3472	141	0.2667	2766	X-RAY DIFFRACTION	95
2.0979-2.1383	0.3332	134	0.2444	2734	X-RAY DIFFRACTION	95
2.1383-2.1819	0.3026	149	0.2477	2769	X-RAY DIFFRACTION	95
2.1819-2.2293	0.3018	140	0.2545	2779	X-RAY DIFFRACTION	95
2.2293-2.2812	0.3035	168	0.2508	2721	X-RAY DIFFRACTION	95
2.2812-2.3382	0.2777	135	0.2243	2761	X-RAY DIFFRACTION	95
2.3382-2.4014	0.3039	145	0.2011	2774	X-RAY DIFFRACTION	96
2.4014-2.4721	0.2569	177	0.2011	2767	X-RAY DIFFRACTION	96
2.4721-2.5518	0.2682	157	0.1991	2815	X-RAY DIFFRACTION	97
2.5518-2.643	0.2758	135	0.2106	2816	X-RAY DIFFRACTION	97
2.643-2.7488	0.235	168	0.1951	2802	X-RAY DIFFRACTION	97
2.7488-2.8738	0.2572	156	0.1946	2804	X-RAY DIFFRACTION	98
2.8738-3.0253	0.2494	170	0.1843	2815	X-RAY DIFFRACTION	97
3.0253-3.2147	0.2393	168	0.1754	2791	X-RAY DIFFRACTION	97
3.2147-3.4627	0.1983	160	0.1713	2831	X-RAY DIFFRACTION	98
3.4627-3.8108	0.2124	141	0.1634	2825	X-RAY DIFFRACTION	97
3.8108-4.3613	0.1737	152	0.1498	2798	X-RAY DIFFRACTION	97
4.3613-5.4913	0.1671	155	0.151	2819	X-RAY DIFFRACTION	97
5.4913-34.8549	0.1966	140	0.192	2858	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	3.8912	2.187	-1.7901	7.1078	-2.7904	6.4935	0.0846	-0.304	-0.1601	0.0626	-0.3108	-0.44	0.2637	0.6032	0.2075	0.1585	0.0577	-0.0112	0.3057	-0.0341	0.2293	6.9842	-7.6714	-15.0037
2	8.8349	2.7696	-0.1273	2.0031	1.2998	8.3804	0.0325	0.4978	-0.5237	-0.3843	0.0649	-0.5192	0.1836	0.6919	-0.0906	0.2574	0.0821	0.0048	0.3331	-0.1067	0.3579	11.5467	-7.5005	-25.4373
3	1.2381	-0.3191	-0.1373	0.7581	-0.1718	1.6961	0.1111	0.1689	-0.0199	-0.0837	-0.0854	-0.0008	0.032	0.0461	-0.0333	0.178	0.0042	-0.0179	0.2046	-0.0245	0.1976	-6.3447	0.987	-18.3328
4	2.4197	0.6075	-0.5455	3.4904	-0.8774	1.9472	0.078	0.0959	0.2218	0.0587	0.0157	-0.3187	-0.0873	0.3173	-0.085	0.1883	-0.0269	-0.0167	0.2687	-0.0219	0.198	2.8838	8.343	-6.262
5	7.3664	2.72	-1.9308	6.9294	-1.5563	8.4059	0.1144	0.1642	-0.3731	-0.2646	-0.2031	-0.1545	0.1122	0.5025	0.1095	0.2681	0.1071	-0.0939	0.2953	-0.0091	0.184	6.8657	-4.781	16.6829
6	3.7361	-1.3269	1.2992	9.1834	0.6704	2.8592	0.147	-0.4302	-0.3686	0.3956	0.179	-0.2678	0.4759	0.1704	-0.3086	0.3932	-0.0097	-0.115	0.3889	0.0089	0.2027	5.9077	-1.4112	27.7719
7	6.0607	-0.5534	-0.6847	1.1171	0.2069	3.3381	-0.0242	-0.2446	0.0052	0.2027	0.0714	0.0612	0.0424	0.0706	-0.0621	0.2853	-0.0069	-0.0113	0.226	-0.0017	0.165	-7.1456	7.2852	21.7601
8	8.9744	-0.8598	-3.1815	1.5185	-0.5685	4.2276	-0.0739	0.5242	-0.0114	-0.1195	0.0997	0.0412	0.0182	-0.0331	-0.024	0.224	-0.0133	-0.0341	0.126	-0.0155	0.1716	-6.137	5.0369	11.2305
9	2.2926	-0.0985	-0.0438	1.6357	0.8503	2.2138	0.2124	-0.2853	-0.0435	0.3098	-0.1451	-0.0026	0.0312	-0.0465	0.0045	0.2859	-0.032	-0.0742	0.2661	0.0026	0.2026	-6.2402	4.9316	13.1399
10	4.2244	1.6026	-0.703	4.1607	-1.7524	3.3941	0.1498	-0.1296	-0.38	0.2716	0.0264	0.1345	0.2876	-0.112	-0.1531	0.2533	0.0161	-0.0093	0.1932	-0.0318	0.1673	-9.1892	-5.8052	6.4729
11	4.3684	-1.1029	0.9516	3.469	2.8423	6.5101	0.1268	-0.0001	0.3111	0.0524	-0.1258	-0.4438	-0.0507	-0.0607	0.0427	0.2345	0.0757	-0.0088	0.2343	0.0925	0.2735	-35.6095	25.4457	-17.0551
12	4.7369	-0.0295	0.5026	6.093	2.2561	9.8129	-0.0357	-0.1275	-0.0515	0.2254	-0.0032	0.3698	0.4712	-0.5491	0.0626	0.1675	-0.0192	-0.039	0.349	0.0559	0.3436	-38.1951	20.0483	-18.512
13	7.6948	-2.2225	-0.2807	2.4506	3.2845	9.1496	0.4661	0.8315	0.3268	-0.3664	-0.5555	0.0969	0.742	-0.8385	0.2421	0.3847	-0.0361	-0.0705	0.5165	0.041	0.3534	-42.872	19.3103	-26.5388
14	2.074	-0.8662	-0.076	3.7499	0.3923	1.0411	0.1758	0.3996	0.2004	-0.2397	-0.0991	0.1139	-0.0772	-0.2547	-0.0788	0.2017	0.0284	-0.0167	0.3819	0.0561	0.2311	-26.5644	12.5584	-25.1619
15	1.743	-0.6075	-0.0017	2.9009	0.5909	1.48	0.1533	0.1563	0.1166	-0.0943	-0.0276	0.041	-0.0968	-0.1408	-0.1121	0.1845	0.0052	0.0136	0.2567	0.054	0.2108	-20.721	12.4884	-18.5145
16	2.7077	-0.3644	1.1153	0.6188	0.6074	1.7027	0.1031	0.3536	0.0723	0.0802	0.2117	0.0906	-0.0489	-0.4006	-0.2438	0.2691	0.0239	0.0386	0.2853	0.0422	0.2162	-28.9644	16.0208	-12.8433
17	5.8795	1.7593	2.8364	4.0968	3.6006	3.4972	0.1531	1.1637	-0.8121	-0.2959	-0.0538	0.3723	0.4197	-0.6336	-0.0623	0.355	-0.1012	-0.0136	0.6399	-0.1242	0.6492	-37.7115	-2.187	-11.1371
18	3.0415	0.4612	-0.2013	2.8854	-0.438	2.8101	-0.0068	0.0585	0.0577	0.0273	0.1972	0.2437	-0.0953	-0.423	-0.1944	0.1674	0.0188	0.0204	0.2385	0.018	0.1892	-29.8176	14.8462	-3.4769
19	6.0755	0.3163	-0.8646	9.7446	-2.6096	9.6194	0.2722	0.0642	0.1945	-0.3665	0.1081	0.4992	-0.7819	-0.4202	-0.3107	0.3804	0.1351	0.0604	0.353	-0.0086	0.3149	-34.0618	30.214	10.7503
20	4.7712	3.5822	0.9021	8.2432	1.75	6.6558	0.2472	-0.1332	0.5443	0.931	0.1159	0.2439	-0.7145	-0.0068	-0.2402	0.4984	0.1305	0.1069	0.4012	-0.0402	0.4874	-30.9728	35.6665	20.2713
21	2.7927	0.7308	-0.6784	7.5118	-1.8934	6.6761	-0.0338	-0.4315	0.7423	0.9224	0.4588	0.699	-0.2695	-0.4392	-0.2751	0.629	0.1537	0.0461	0.4616	-0.1542	0.5135	-31.9222	30.7907	23.12
22	2.5449	-0.4591	-0.6776	1.3173	0.1432	2.708	0.0295	-0.1578	0.2201	0.2101	0.0795	0.0582	-0.2609	-0.2032	-0.0983	0.2792	0.0109	0.0205	0.2144	-0.0215	0.2129	-20.8757	19.2928	17.7026
23	3.4029	1.3632	0.4872	4.0598	-0.1801	1.7429	0.3139	-0.6284	0.5627	0.3556	-0.3	-0.3244	-0.4892	0.2803	-0.0161	0.3525	-0.04	0.0432	0.3225	-0.1338	0.3916	-17.8685	27.6661	7.6202
24	4.9152	2.2476	-0.4476	5.345	-0.5434	1.7966	0.0967	0.0081	0.4856	0.2258	0.068	0.0767	-0.3259	-0.0117	-0.153	0.2348	0.0196	0.0214	0.2053	-0.0067	0.2025	-22.9736	24.1766	-0.114

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:40)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 41:59)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 60:195)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 196:252)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 3:40)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 41:78)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 79:126)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 127:148)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 149:195)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 196:253)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 3:17)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 18:40)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 41:59)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 60:101)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 102:168)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 169:193)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 194:209)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 210:251)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 3:29)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 30:50)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 51:64)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 65:168)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 169:209)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 210:251)

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