+Open data
-Basic information
Entry | Database: PDB / ID: 1h2a | ||||||
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Title | SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS | ||||||
Components | (HYDROGENASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NI-FE HYDROGENASE / SO LIGAND / HYDROGEN METABOLISM / MG CENTER / MIR / MAD | ||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 1.8 Å | ||||||
Authors | Higuchi, Y. / Yasuoka, N. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis. Authors: Higuchi, Y. / Yagi, T. / Yasuoka, N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Location of Active Sites of Nife Hydrogenase Determined by the Combination of Multiple Isomorphous Replacement and Multiwavelength Anomalous-Diffraction Methods Authors: Higuchi, Y. / Okamoto, T. / Fujimoto, K. / Misaki, S. / Morimoto, Y. / Yasouka, N. #2: Journal: J.Biol.Chem. / Year: 1987 Title: Single Crystals of Hydrogenase from Desulfovibrio Vulgaris Miyazaki F Authors: Higuchi, Y. / Yasuoka, N. / Kakudo, M. / Katsube, Y. / Yagi, T. / Inokuchi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h2a.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h2a.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 1h2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h2a_validation.pdf.gz | 421.1 KB | Display | wwPDB validaton report |
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Full document | 1h2a_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 1h2a_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1h2a_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h2a ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h2a | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules SL
#1: Protein | Mass: 34148.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IAM 12604 Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P21853, 1.18.99.1 |
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#2: Protein | Mass: 62711.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IAM 12604 Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P21852, 1.18.99.1 |
-Non-polymers , 5 types, 643 molecules
#3: Chemical | #4: Chemical | ChemComp-F3S / | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-NFE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: microdialysis / Details: Higuchi, Y., (1987) J.Biol.Chem., 262, 2823. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Detector: IMAGE PLATE |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 251414 / % possible obs: 81.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.105 / Rsym value: 0.041 |
Reflection shell | Resolution: 1.8→1.88 Å / % possible all: 46 |
Reflection | *PLUS Num. obs: 63133 / Num. measured all: 251414 |
Reflection shell | *PLUS % possible obs: 46 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR, MAD / Resolution: 1.8→20 Å / σ(F): 1
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Displacement parameters | Biso mean: 24.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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