PDB-4h15: Crystal Structure of a short chain alcohol dehydrogenase-related ...

ID or keywords:

Entry

Database: PDB / ID: 4h15

Title

Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P21

Components

Short chain alcohol dehydrogenase-related dehydrogenase

Keywords

OXIDOREDUCTASE / Structural Genomics / PSI-Biology / NYSGRC / New York Structural Genomics Research Consortium

Function / homology

Function and homology information

Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

Sinorhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.45 Å

Authors

Ghosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)

Citation

Journal: To be Published
Title: Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P21
Authors: Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium

History

Deposition	Sep 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4h15.cif.gz	418.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4h15.ent.gz	359.6 KB	Display	PDB format
PDBx/mmJSON format	4h15.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/h1/4h15 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/4h15	HTTPS FTP

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Related structure data

Related structure data	4h16
Similar structure data	4h16-1 3vdq-d 5idx-1 3w8f-1 3aut-1 5idy-1 1hxh-d 5b4t-1 5b4u-1 2cfc-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-011812

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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: Short chain alcohol dehydrogenase-related dehydrogenase

B: Short chain alcohol dehydrogenase-related dehydrogenase

C: Short chain alcohol dehydrogenase-related dehydrogenase

D: Short chain alcohol dehydrogenase-related dehydrogenase

hetero molecules

113 kDa, 4 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)	65.304, 119.143, 67.156
Angle α, β, γ (deg.)	90.000, 105.830, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

There is 1 biological unit (a tetramer) in the asymmetric unit (chain A, B, C, D)

#1: Protein	Short chain alcohol dehydrogenase-related dehydrogenase Mass: 27486.529 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0888, SMa1629 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL References: UniProt: Q92YJ2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 941 / 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: 2.29 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Calcium Chloride 0.1 M Bis-Tris:HCl, 45% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 77 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X9A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2012

Radiation

Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 1.45→50 Å / Num. obs: 170863 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / B_iso Wilson estimate: 12.4 Å² / R_merge(I) obs: 0.03 / Χ²: 1.106 / Net I/σ(I): 27.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.45-1.48	2.1	0.148	16049	1.307	1	93.8
1.48-1.5	2.1	0.13	16178	1.25	1	94.2
1.5-1.53	2.1	0.115	16330	1.221	1	94.7
1.53-1.56	2.1	0.098	16470	1.141	1	95.1
1.56-1.6	2.1	0.089	16469	1.094	1	95.6
1.6-1.63	2.1	0.08	16517	1.278	1	95.8
1.63-1.67	2.1	0.071	16644	1.203	1	96.4
1.67-1.72	2.1	0.063	16573	1.123	1	96.8
1.72-1.77	2.1	0.057	16744	1.07	1	97.2
1.77-1.83	2.1	0.05	16781	0.977	1	97.6
1.83-1.89	2.1	0.043	16888	1.012	1	98
1.89-1.97	2.1	0.038	16947	1.006	1	98.3
1.97-2.06	2.1	0.033	16982	1.046	1	98.7
2.06-2.17	2.1	0.031	17088	1.098	1	98.9
2.17-2.3	2.1	0.032	17030	1.044	1	98.9
2.3-2.48	2.1	0.034	17080	1.048	1	99.2
2.48-2.73	2	0.031	17039	1.001	1	99.1
2.73-3.12	2	0.023	16848	1.004	1	97.8
3.12-3.94	1.9	0.018	16172	1.115	1	93.9
3.94-50	2	0.017	14507	1.068	1	84.1

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
CBASS		data collection
HKL-3000		data reduction
SOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.45→27.787 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.9082 / SU ML: 0.11 / σ(F): 1.35 / Phase error: 15.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1672	8550	5 %	RANDOM
R_work	0.1496	-	-	-
obs	0.1505	170860	98.05 %	-
all	-	170863	-	-

Solvent computation

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

Displacement parameters

B_iso max: 78.05 Å² / B_iso mean: 16.9524 Å² / B_iso min: 3.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→27.787 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7632	0	147	941	8720

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8174
X-RAY DIFFRACTION	f_angle_d	1.161	11174
X-RAY DIFFRACTION	f_chiral_restr	0.074	1348
X-RAY DIFFRACTION	f_plane_restr	0.006	1441
X-RAY DIFFRACTION	f_dihedral_angle_d	12.788	3091

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4499-1.4664	0.1984	254	0.1717	4938	5192	90
1.4664-1.4836	0.2069	278	0.172	5526	5804	99
1.4836-1.5017	0.1988	268	0.1678	5454	5722	100
1.5017-1.5207	0.1944	272	0.1723	5559	5831	100
1.5207-1.5407	0.1677	292	0.1612	5429	5721	100
1.5407-1.5618	0.1847	289	0.1524	5564	5853	100
1.5618-1.5841	0.1663	284	0.1476	5406	5690	100
1.5841-1.6078	0.1702	292	0.1479	5510	5802	100
1.6078-1.6329	0.1666	305	0.1456	5544	5849	100
1.6329-1.6597	0.1854	279	0.1429	5451	5730	100
1.6597-1.6883	0.1438	288	0.1446	5482	5770	100
1.6883-1.719	0.174	303	0.1506	5513	5816	100
1.719-1.752	0.1739	271	0.1518	5492	5763	100
1.752-1.7878	0.1573	309	0.1555	5465	5774	100
1.7878-1.8267	0.1685	283	0.1443	5507	5790	100
1.8267-1.8692	0.1718	301	0.1453	5506	5807	100
1.8692-1.9159	0.1632	287	0.1473	5540	5827	100
1.9159-1.9677	0.1604	294	0.1505	5440	5734	100
1.9677-2.0256	0.1795	307	0.1471	5493	5800	100
2.0256-2.0909	0.159	300	0.1403	5485	5785	100
2.0909-2.1656	0.1716	283	0.1443	5543	5826	100
2.1656-2.2523	0.1533	321	0.1367	5414	5735	99
2.2523-2.3547	0.1585	281	0.1385	5500	5781	99
2.3547-2.4788	0.1616	286	0.1424	5500	5786	99
2.4788-2.634	0.1672	292	0.1492	5453	5745	99
2.634-2.8372	0.1718	266	0.1415	5507	5773	99
2.8372-3.1224	0.1646	265	0.1445	5392	5657	97
3.1224-3.5734	0.1539	284	0.1424	5177	5461	94
3.5734-4.499	0.1485	281	0.1447	4947	5228	89
4.499-27.792	0.2036	235	0.1947	4573	4808	81

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	1.8128	0.8016	0.4166	0.5556	-0.157	1.5923	0.0622	-0.1774	-0.1686	0.2797	-0.0141	-0.3591	0.1594	0.063	-0.0271	0.1817	0.0189	-0.0746	0.1355	0.0435	0.1488	-15.5072	8.1468	1.2146
2	0.3541	-0.5102	-0.0399	1.0893	0.6961	1.0752	0.0928	-0.2641	-0.3076	0.5818	-0.0479	0.1089	0.35	-0.0617	-0.047	0.2863	-0.0223	-0.0434	0.1767	0.0647	0.1713	-25.9055	-1.2285	2.9006
3	0.5046	-0.0937	-0.2382	0.6191	0.1226	0.8286	0.0211	-0.0857	-0.0654	0.1325	-0.0029	-0.0253	0.0831	0.011	-0.0048	0.0686	-0.0041	-0.0155	0.0575	0.0151	0.0625	-28.4829	5.5564	-13.695
4	1.4692	-0.177	0.0051	0.9603	-0.3015	1.3856	-0.0094	0.1247	-0.1489	-0.0326	-0.0733	-0.1765	0.1285	0.2739	0.0505	0.0637	0.0106	-0.0104	0.0874	0.001	0.1109	-14.6099	14.7024	-19.0385
5	1.1508	0.744	1.1145	2.2372	1.9222	2.4777	0.0991	0.0363	-0.0162	-0.054	-0.1156	0.205	0.1694	-0.1764	0.0005	0.1558	0.0133	-0.0475	0.108	0.024	0.0916	-51.5235	24.847	-49.1496
6	1.3794	0.066	0.7857	2.5371	1.1603	2.1411	-0.2505	0.4674	0.3642	-0.7755	0.2557	-0.2136	-0.7042	0.1798	0.0745	0.3398	-0.0403	-0.0445	0.1699	0.0561	0.1891	-46.9906	40.8411	-50.3225
7	3.1919	0.5158	-0.3075	2.2032	-0.5581	1.0144	-0.0088	0.1245	0.4851	-0.0964	-0.0729	0.4177	-0.5066	-0.191	0.0436	0.2198	0.0486	-0.0498	0.1311	0.0081	0.1581	-52.9067	42.8058	-41.4998
8	0.812	0.1714	0.0978	0.6905	-0.0119	0.3697	-0.0244	0.0299	0.0669	-0.064	0.0034	0.0574	-0.0605	-0.0308	0.0156	0.0581	0.0062	0.0016	0.0457	0.0001	0.0435	-39.0018	35.0021	-33.0002
9	5.5029	1.4971	-3.0964	1.8653	-0.6673	3.5156	0.1158	0.7632	0.6503	-0.8004	-0.231	-0.412	0.0826	0.3151	0.1311	0.314	-0.0107	0.1075	0.3853	0.1032	0.3389	-19.8006	27.3192	-49.5486
10	1.7096	-0.3239	0.0522	0.7444	-0.1101	1.0549	0.0624	0.1071	-0.033	-0.1189	-0.0174	0.0267	-0.0011	-0.0057	-0.0333	0.0517	-0.0042	-0.0034	0.0189	-0.004	0.0276	-39.9646	20.4113	-40.0755
11	2.2376	-0.717	0.8058	2.3409	-0.9158	2.8709	-0.026	0.226	0.1156	-0.4419	-0.0374	0.2741	-0.1159	-0.0351	0.0437	0.1746	-0.0349	-0.0582	0.0979	-0.0212	0.1686	-51.699	6.1717	-44.954
12	2.1781	0.1749	0.8411	1.1848	0.0441	0.3518	0.0974	-0.1599	-0.3879	-0.0242	0.2756	0.2828	0.3477	-0.4492	-0.2841	0.1724	-0.0604	-0.0399	0.1523	0.0292	0.202	-52.4561	-7.6818	-37.3734
13	2.1772	-0.2335	-0.3839	4.3444	0.1345	4.2217	-0.0255	0.1329	-0.5052	-0.4196	-0.0805	-0.2768	0.5841	0.1744	0.0442	0.138	0	0.0282	0.1041	-0.04	0.1982	-41.3214	-8.6833	-40.0276
14	0.3509	-0.1524	0.5239	0.4238	-0.983	4.4217	0.0957	-0.0932	-0.0465	-0.0037	-0.0148	0.0747	0.3009	-0.1973	-0.1009	0.1133	-0.0351	0.0091	0.0825	0.02	0.098	-42.7545	-1.8062	-16.065
15	3.8268	0.5053	-2.6242	2.6048	-0.0543	6.2455	-0.0138	0.0757	-0.2811	-0.1449	-0.08	-0.122	0.4142	-0.1347	0.0398	0.0704	0.0017	-0.0072	0.0456	-0.0198	0.0957	-34.4233	-3.6072	-36.7077
16	0.5876	0.0376	0.066	0.8959	0.0702	0.7499	0.0219	-0.015	-0.0615	-0.0163	-0.0013	0.0308	0.0835	-0.0439	-0.0109	0.032	-0.0047	-0.0087	0.0328	0.0038	0.0431	-38.9413	7.9284	-28.3468
17	6.3376	-1.0937	-3.5434	4.7211	1.124	7.3564	-0.0242	-0.6695	-0.6847	0.766	-0.1917	0.5724	0.9827	-0.4069	0.197	0.306	-0.0829	0.0134	0.2112	0.0618	0.3334	-61.4054	5.0892	-15.8052
18	1.0116	0.0988	0.1779	1.0453	0.3452	0.8192	0.0086	-0.1201	-0.0277	0.0393	-0.0626	0.187	0.0311	-0.2112	0.0215	0.0329	-0.0026	-0.0011	0.0754	0.0053	0.0748	-51.059	15.4081	-27.8232
19	1.344	0.0618	0.7224	1.2198	0.1679	2.2594	-0.0078	-0.0929	0.0972	0.247	0.0139	-0.1823	-0.1256	0.094	-0.0069	0.1686	-0.0324	-0.0125	0.0994	-0.0258	0.1021	-18.363	43.3192	-5.8599
20	0.7054	0.0406	0.1874	0.8096	0.0194	0.5144	-0.0229	-0.0742	0.0776	0.0496	-0.0061	-0.029	-0.0744	0.0072	0.02	0.0607	0.0004	0.003	0.0497	-0.0064	0.0411	-29.2957	37.5211	-19.1636
21	0.9812	-0.9569	0.2876	1.7724	0.848	1.7258	-0.1973	-1.1363	0.6459	0.8664	-0.1738	0.9683	-0.115	-0.727	0.3399	0.3662	0.0659	0.055	0.5217	-0.1924	0.552	-48.6447	36.4117	-1.7276
22	1.7714	0.4957	-0.3316	0.8968	0.265	1.1046	0.0499	-0.1401	-0.0189	0.1617	-0.045	-0.0277	-0.0115	-0.0087	-0.001	0.0808	0.0003	-0.0081	0.0458	0.0153	0.0266	-28.6643	26.1674	-7.7745

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 59 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 82 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 186 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 187 through 259 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -1 through 31 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 32 through 59 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 82 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 186 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 187 through 215 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 216 through 259 )	B
11	X-RAY DIFFRACTION	11	chain 'C' and (resid -1 through 31 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 32 through 59 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 60 through 82 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 83 through 110 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 111 through 127 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 128 through 186 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 187 through 200 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 201 through 259 )	C
19	X-RAY DIFFRACTION	19	chain 'D' and (resid -1 through 82 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 83 through 186 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 187 through 214 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 215 through 259 )	D

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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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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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi