PDB-4gic: Crystal Structure Of a Putative Histidinol dehydrogenase (Target ...

ID or keywords:

Entry

Database: PDB / ID: 4gic

Title

Crystal Structure Of a Putative Histidinol dehydrogenase (Target PSI-014034) from Methylococcus capsulatus

Components

Histidinol dehydrogenase

Keywords

OXIDOREDUCTASE / Histidinol /

dehydrogenase /

Protein structure initiative /

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

Function / homology

Function and homology information

histidinol dehydrogenase /

histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding
Similarity search - Function

Biological species

Methylococcus capsulatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

molecular replacement / Resolution: 2.052 Å

Authors

Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. ...

Citation

Journal: to be published
Title: Crystal structure of a putative Histidinol dehydrogenase from Methylococcus capsulatus
Authors: Kumar, P.R. / Hillerich, B. / Love, J. / Seidel, R. / Almo, S.C.

History

Deposition	Aug 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4gic.cif.gz	293.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/4gic ftp://data.pdbj.org/pub/pdb/validation_reports/gi/4gic	HTTPS FTP

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Related structure data

Similar structure data	6d9l-1 6d92-1 6d8p-1 6d9k-2 5awh-1 6d92-2 6d9l-2 6d8a-2 6d8p-2 6d9k-1 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-014034

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Links

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

Deposited unit

A: Histidinol dehydrogenase

B: Histidinol dehydrogenase

hetero molecules

92 kDa, 2 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)	78.040, 81.517, 147.036
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

The biological assembly is a dimer

#1: Protein	Histidinol dehydrogenase / / HDH Mass: 45910.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: Bath / Gene: hisD, MCA1963 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q606Q2, histidinol dehydrogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.55 Å³/Da / Density % sol: 51.7 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Li2SO4, 0.1M Tris-HCl, 30% PEG 3350 - MCSG4 #70); Cryoprotection (Li2SO4), Sitting Drop, Vapor Diffusion, temperature ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Li2SO4, 0.1M Tris-HCl, 30% PEG 3350 - MCSG4 #70); Cryoprotection (Li2SO4), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal

Density Matthews: 2.55 Å³/Da / Density % sol: 51.7 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Li2SO4, 0.1M Tris-HCl, 30% PEG 3350 - MCSG4 #70); Cryoprotection (Li2SO4), Sitting Drop, Vapor Diffusion, temperature ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2011 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.05→50 Å / Num. obs: 113265 / % possible obs: 100 % / Redundancy: 4.2 % / R_merge(I) obs: 0.089 / Χ²: 1.552 / Net I/σ(I): 18.83

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all	R_merge(I) obs
2.05-2.09	4.1	1.16	5631	1.253	100
2.09-2.12	4.1		5677	1.261	100
2.12-2.16	4.2		5653	1.275	100
2.16-2.21	4.2		5680	1.305	100	0.948
2.21-2.26	4.2		5682	1.361	100	0.783
2.26-2.31	4.2		5622	1.271	100	0.755
2.31-2.37	4.2		5647	1.283	100	0.571
2.37-2.43	4.2		5665	1.263	100	0.502
2.43-2.5	4.2		5720	1.288	100	0.423
2.5-2.58	4.2		5626	1.318	100	0.348
2.58-2.68	4.3		5680	1.344	100	0.282
2.68-2.78	4.3		5682	1.356	100	0.219
2.78-2.91	4.2		5664	1.39	100	0.176
2.91-3.06	4.2		5638	1.504	100	0.134
3.06-3.25	4.2		5690	1.621	100	0.102
3.25-3.51	4.2		5651	1.959	100	0.081
3.51-3.86	4.2		5682	2.257	100	0.064
3.86-4.42	4.1		5648	2.282	100	0.051
4.42-5.56	4.1		5662	2.253	100	0.045
5.56-50	4.2		5665	2.216	99.4	0.039

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Phasing

Phasing

Method
SAD
molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
SHELX		phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
CBASS		data collection
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.052→42.004 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7987 / SU ML: 0.25 / σ(F): 0 / Phase error: 26.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2282	2723	5.04 %	RANDOM
R_work	0.1933	-	-	-
obs	0.1951	53989	90.92 %	-

Solvent computation

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

Displacement parameters

B_iso max: 149.64 Å² / B_iso mean: 40.7746 Å² / B_iso min: 12.32 Å²

Refinement step

Cycle: LAST / Resolution: 2.052→42.004 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5800	0	10	187	5997

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5928
X-RAY DIFFRACTION	f_angle_d	1.119	8058
X-RAY DIFFRACTION	f_chiral_restr	0.071	936
X-RAY DIFFRACTION	f_plane_restr	0.005	1056
X-RAY DIFFRACTION	f_dihedral_angle_d	12.504	2184

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0523-2.0896	0.359	131	0.3289	2268	2399	78
2.0896-2.1298	0.3342	132	0.2936	2349	2481	80
2.1298-2.1732	0.2889	125	0.2826	2418	2543	83
2.1732-2.2205	0.2995	141	0.2586	2491	2632	85
2.2205-2.2721	0.2898	121	0.2458	2537	2658	86
2.2721-2.329	0.3245	127	0.2478	2503	2630	85
2.329-2.3919	0.29	140	0.2168	2556	2696	88
2.3919-2.4623	0.2516	146	0.2159	2599	2745	88
2.4623-2.5418	0.2921	134	0.2109	2609	2743	89
2.5418-2.6326	0.3196	132	0.2215	2681	2813	91
2.6326-2.738	0.2531	162	0.2106	2715	2877	93
2.738-2.8626	0.2551	138	0.2129	2736	2874	92
2.8626-3.0134	0.2672	155	0.2118	2838	2993	95
3.0134-3.2022	0.2339	149	0.2144	2899	3048	98
3.2022-3.4493	0.2296	154	0.195	2924	3078	98
3.4493-3.7962	0.2082	146	0.1673	2975	3121	99
3.7962-4.3451	0.1651	157	0.1486	2989	3146	99
4.3451-5.4724	0.1829	165	0.1545	3015	3180	99
5.4724-42.0131	0.2076	168	0.1846	3164	3332	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	2.4711	-0.202	-0.3827	2.8153	-1.1316	3.5456	-0.0864	-0.1344	0.088	-0.1364	0.4633	0.4919	0.5217	-0.8206	-0.3228	0.3749	-0.1081	-0.0751	0.4808	0.0543	0.3884	40.1189	14.1939	53.0207
2	1.7831	-0.0242	-0.3116	1.7053	-0.2598	2.8588	0.0209	-0.1015	0.078	0.1345	0.0197	0.1479	-0.1626	-0.2375	-0.0484	0.2575	0.0142	-0.0508	0.2141	-0.0227	0.1528	57.1459	44.6332	68.6584
3	5.7216	-1.2411	-1.2423	5.4077	-0.8024	1.9248	-0.1166	-0.5821	-0.2884	0.3941	0.2407	0.1123	0.5938	-0.1394	-0.0715	0.443	-0.0914	-0.0396	0.3106	0.0711	0.2282	50.6861	10.5159	61.8827
4	1.8474	0.8717	-0.159	2.9181	-0.3912	1.5435	0.0315	-0.1942	-0.2209	0.1061	0.0083	0.0738	0.2221	-0.1631	-0.0252	0.2588	-0.0024	-0.0392	0.2349	0.0252	0.149	56.1636	22.3527	55.31
5	6.2639	2.6424	-0.2821	8.0362	1.8756	8.0706	0.1388	-0.2169	0.7105	0.0908	-0.1734	1.493	-0.5651	-0.6721	0.0482	0.1326	0.0133	-0.0019	0.3294	-0.0101	0.3449	35.1028	41.2295	40.4057
6	3.9603	0.7085	-1.2043	3.7663	-0.7873	5.3137	0.0426	0.6316	-0.0727	-0.6959	0.0242	0.557	0.0396	-0.5349	-0.0505	0.2777	0.031	-0.1122	0.3393	-0.0171	0.193	40.3524	36.3835	24.7693
7	2.8548	0.0512	3.1665	0.005	-0.0201	6.5406	-0.09	0.5886	-0.0073	-0.4397	0.0975	-0.217	-0.5108	0.68	-0.0243	0.3911	-0.0235	0.0533	0.3217	0.0475	0.2365	68.3239	42.3461	24.7673
8	2.687	-0.0995	1.6376	1.1101	-0.2878	3.8864	0.148	0.1753	-0.0165	-0.0534	-0.0974	-0.0359	0.0102	0.2934	-0.0165	0.1977	0.0113	-0.0007	0.1394	-0.013	0.1245	58.1248	35.8813	36.6412
9	1.9053	2.601	0.5899	5.7496	-0.1409	1.2187	-0.0815	0.2066	0.0997	-0.2979	-0.046	-0.5219	-0.2112	0.2189	0.0992	0.3412	0.0433	0.0515	0.272	0.0184	0.3524	59.1288	56.7552	41.5867
10	3.9965	0.1626	1.1168	2.3124	0.698	3.965	0.238	0.662	0.3742	-0.1873	-0.0013	-0.1048	-0.6219	0.0773	-0.2669	0.5767	0.0156	0.0228	0.2889	0.1169	0.5442	60.7422	71.2924	39.408
11	2.0198	0.2744	-0.1478	4.9952	-0.2069	1.8177	0.1022	0.0226	0.339	-0.0171	-0.1562	-0.4235	-0.3321	0.311	0.0498	0.2782	-0.0322	-0.022	0.2403	0.0205	0.2047	67.887	51.2348	50.4357

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 31 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 242 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 243 through 294 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 295 through 400 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 31 through 48 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 49 through 74 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 75 through 106 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 107 through 219 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 220 through 265 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 266 through 318 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 319 through 402 )	B

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