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Yorodumi- PDB-3ayz: Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ayz | ||||||
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Title | Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an air-oxidized condition | ||||||
Components | (Membrane-bound hydrogenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / MEMBRANE-BOUND NI-FE HYDROGENASE | ||||||
Function / homology | Function and homology information hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Hydrogenovibrio marinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Shomura, Y. / Yoon, K.S. / Nishihara, H. / Higuchi, Y. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase Authors: Shomura, Y. / Yoon, K.S. / Nishihara, H. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ayz.cif.gz | 769.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ayz.ent.gz | 621.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ayz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/3ayz ftp://data.pdbj.org/pub/pdb/validation_reports/ay/3ayz | HTTPS FTP |
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-Related structure data
Related structure data | 3ayxSC 5y34C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Membrane-bound hydrogenase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 66574.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenovibrio marinus (bacteria) / Strain: MH-110 / References: UniProt: F2Z6J6, EC: 1.12.5.1 #2: Protein | Mass: 31306.662 Da / Num. of mol.: 2 / Fragment: UNP residues 41-323 / Source method: isolated from a natural source / Source: (natural) Hydrogenovibrio marinus (bacteria) / Strain: MH-110 / References: UniProt: F2Z6J5, EC: 1.12.5.1 |
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-Non-polymers , 12 types, 1665 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CYN / #7: Chemical | ChemComp-O / #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.94 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M PIPES, 15% PEG 3350, 300mM lithium sulfate, 5mM DTT, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→20 Å / Num. all: 582417 / Num. obs: 578159 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.22→1.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AYX Resolution: 1.22→20 Å / Num. parameters: 140969 / Num. restraintsaints: 174515 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: 1. The SF file contains friedel pairs. Friedel pairs were independently treated during refinement. Statistics for data collection were calculated from data of which the friedel pairs were ...Details: 1. The SF file contains friedel pairs. Friedel pairs were independently treated during refinement. Statistics for data collection were calculated from data of which the friedel pairs were merged. 2. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 52 / Occupancy sum hydrogen: 13111 / Occupancy sum non hydrogen: 15255.7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→20 Å
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Refine LS restraints |
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