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Yorodumi- PDB-5y34: Membrane-bound respiratory [NiFe]-hydrogenase from Hydrogenovibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y34 | ||||||||||||||||||
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Title | Membrane-bound respiratory [NiFe]-hydrogenase from Hydrogenovibrio marinus in a ferricyanide-oxidized condition | ||||||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / MEMBRANE-BOUND NI-FE HYDROGENASE | ||||||||||||||||||
Function / homology | Function and homology information hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Hydrogenovibrio marinus (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||||||||||||||
Authors | Shomura, Y. / Yoon, K.S. / Nishihara, H. / Higuchi, Y. | ||||||||||||||||||
Funding support | Japan, 5items
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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 | 5y34.cif.gz | 798.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y34.ent.gz | 650.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y34_validation.pdf.gz | 520.3 KB | Display | wwPDB validaton report |
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Full document | 5y34_full_validation.pdf.gz | 531.3 KB | Display | |
Data in XML | 5y34_validation.xml.gz | 82.7 KB | Display | |
Data in CIF | 5y34_validation.cif.gz | 128.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/5y34 ftp://data.pdbj.org/pub/pdb/validation_reports/y3/5y34 | HTTPS FTP |
-Related structure data
Related structure data | 3ayxSC 3ayzC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 66574.398 Da / Num. of mol.: 2 / Fragment: UNP residues 1-596 / Source method: isolated from a natural source / Source: (natural) Hydrogenovibrio marinus (bacteria) / 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) / References: UniProt: F2Z6J5, UniProt: A0A066ZR71*PLUS |
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-Non-polymers , 9 types, 2207 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: 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 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M PIPES, 15% PEG 3350, 300MM LITHIUM SULFATE, 5MM DTT, PH 6.5 |
-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 MX-225 / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→20 Å / Num. obs: 459508 / % possible obs: 99.2 % / Redundancy: 3.8 % / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.2 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AYX Resolution: 1.32→19.89 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.829 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.001 Å2
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Refinement step | Cycle: 1 / Resolution: 1.32→19.89 Å
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Refine LS restraints |
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