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- PDB-4h16: Crystal Structure of a short chain alcohol dehydrogenase-related ... -

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Open data

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Basic information

Entry

Database: PDB / ID: 4h16

Title

Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P6422

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 /

MOLECULAR REPLACEMENT / Resolution: 2 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 P6422
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

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	4h16.cif.gz	113.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4h16.ent.gz	93.3 KB	Display	PDB format
PDBx/mmJSON format	4h16.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/h1/4h16 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/4h16	HTTPS FTP

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Related structure data

Related structure data	4h15
Similar structure data	5idx-1 5va8-d 4h15-d 5itw-d 3t4x-1 2i4l-1 3vdq-d 3tzh-1 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: 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)

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Assembly

Deposited unit

A: Short chain alcohol dehydrogenase-related dehydrogenase

hetero molecules

28.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Short chain alcohol dehydrogenase-related dehydrogenase

hetero molecules

A: Short chain alcohol dehydrogenase-related dehydrogenase

hetero molecules

A: Short chain alcohol dehydrogenase-related dehydrogenase

hetero molecules

A: Short chain alcohol dehydrogenase-related dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	129.2, 129.2, 103.5
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	181
Space group name H-M	P6₄22

Components on special symmetry positions

ID	Model	Components
1	1	A-631- HOH

Details

The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -x,-y-1,z; x,x-y-1,-z-1/3 and -x,-x+y,-z-1/3

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Components

#1: Protein	Short chain alcohol dehydrogenase-related dehydrogenase Mass: 27486.529 Da / Num. of mol.: 1 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-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.54 Å³/Da / Density % sol: 72.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Magnesium Chloride 0.1 M HEPES:NaOH pH 7.5, and 30% (v/v) PPG P400, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction

Mean temperature: 77 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 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: 2→50 Å / Num. obs: 65029 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / B_iso Wilson estimate: 36 Å² / R_merge(I) obs: 0.097 / Χ²: 1.414 / Net I/σ(I): 12.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2-2.03	4.5	0.884	3259	1.407	1	100
2.03-2.07	4.5	0.744	3291	1.393	1	100
2.07-2.11	4.6	0.617	3239	1.503	1	100
2.11-2.15	4.6	0.573	3265	1.46	1	100
2.15-2.2	4.6	0.47	3252	1.49	1	100
2.2-2.25	4.6	0.374	3246	1.572	1	100
2.25-2.31	4.7	0.346	3289	1.569	1	100
2.31-2.37	4.7	0.3	3233	1.603	1	100
2.37-2.44	4.7	0.273	3298	1.644	1	100
2.44-2.52	4.7	0.221	3254	1.623	1	100
2.52-2.61	4.7	0.204	3250	1.535	1	100
2.61-2.71	4.7	0.169	3287	1.488	1	100
2.71-2.84	4.7	0.15	3241	1.484	1	100
2.84-2.99	4.7	0.129	3261	1.42	1	100
2.99-3.17	4.7	0.11	3264	1.309	1	99.9
3.17-3.42	4.7	0.1	3267	1.294	1	99.8
3.42-3.76	4.7	0.087	3234	1.179	1	99
3.76-4.31	4.6	0.074	3220	1.028	1	98.4
4.31-5.43	4.5	0.06	3187	1.096	1	97.4
5.43-50	4.7	0.038	3192	1.139	1	97.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Code:

Resolution: 2→37.294 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.19 / σ(F): 1.91 / Phase error: 17.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1781	3266	5.03 %	RANDOM
R_work	0.1629	-	-	-
obs	0.1636	64983	99.57 %	-

Solvent computation

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

Displacement parameters

B_iso max: 148.62 Å² / B_iso mean: 30.2639 Å² / B_iso min: 7.4 Å²

Refinement step

Cycle: LAST / Resolution: 2→37.294 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1886	0	42	235	2163

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1999
X-RAY DIFFRACTION	f_angle_d	1.078	2706
X-RAY DIFFRACTION	f_chiral_restr	0.068	319
X-RAY DIFFRACTION	f_plane_restr	0.005	349
X-RAY DIFFRACTION	f_dihedral_angle_d	17.923	764

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0005-2.0303	0.3288	137	0.2809	2682	2819	100
2.0303-2.062	0.2981	145	0.2595	2694	2839	100
2.062-2.0958	0.2641	135	0.2249	2710	2845	100
2.0958-2.132	0.2347	136	0.2147	2662	2798	100
2.132-2.1707	0.2103	150	0.2094	2709	2859	100
2.1707-2.2125	0.1826	140	0.1968	2692	2832	100
2.2125-2.2576	0.2413	149	0.2	2707	2856	100
2.2576-2.3067	0.202	145	0.1832	2715	2860	100
2.3067-2.3604	0.2262	149	0.1673	2657	2806	100
2.3604-2.4194	0.2124	121	0.1689	2715	2836	100
2.4194-2.4848	0.1703	146	0.1642	2701	2847	100
2.4848-2.5579	0.2	137	0.16	2670	2807	100
2.5579-2.6404	0.2368	142	0.1558	2712	2854	100
2.6404-2.7348	0.1619	131	0.1454	2696	2827	100
2.7348-2.8442	0.1791	165	0.1482	2679	2844	100
2.8442-2.9736	0.185	138	0.1475	2693	2831	100
2.9736-3.1303	0.1557	151	0.1509	2709	2860	100
3.1303-3.3263	0.1781	142	0.1436	2666	2808	100
3.3263-3.583	0.1387	148	0.1412	2680	2828	99
3.583-3.9432	0.1252	163	0.1243	2662	2825	99
3.9432-4.5129	0.162	138	0.1328	2612	2750	97
4.5129-5.6826	0.1637	136	0.1554	2653	2789	98
5.6826-37.3007	0.1973	122	0.2115	2641	2763	97

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	3.1261	0.478	-0.0932	1.031	-0.3862	1.1902	0.0037	-0.8114	0.1896	0.3295	-0.1517	-0.0608	-0.1217	0.1025	0.0965	0.0939	-0.0242	-0.0491	0.5089	-0.0464	0.1456	50.3343	-45.2539	8.2559
2	1.3172	-0.044	0.0911	1.329	-0.0047	1.2102	-0.0541	-0.3238	-0.0112	0.0129	-0.0444	-0.1074	-0.1299	0.2729	0.0949	0.0622	0.0154	-0.016	0.1748	0.0101	0.1407	47.0381	-46.9968	-9.6889
3	2.7346	-0.0674	0.0553	0.6341	0.0587	3.3904	-0.0372	-0.6078	0.8028	-0.0013	-0.1708	-0.0765	-1.1297	0.0111	-0.0345	0.0694	0.0634	-0.0594	0.1999	-0.1529	0.335	31.9001	-42.0778	-2.7225

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 82 )	A	0
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 172 )	A	0
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 173 through 259 )	A	0

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