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Yorodumi- PDB-6yf4: [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yf4 | ||||||
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Title | [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI), variant E279D | ||||||
Components | Iron hydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / [FeFe]-hydrogenase / Clostridium pasteurianum / E279D | ||||||
Function / homology | Function and homology information ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Duan, J. / Hofmann, E. / Happe, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases. Authors: Lampret, O. / Duan, J. / Hofmann, E. / Winkler, M. / Armstrong, F.A. / Happe, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yf4.cif.gz | 455.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yf4.ent.gz | 367.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yf4_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6yf4_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6yf4_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 6yf4_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/6yf4 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/6yf4 | HTTPS FTP |
-Related structure data
Related structure data | 4xdcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 65097.379 Da / Num. of mol.: 2 / Mutation: E279D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): delta-iscR / References: UniProt: P29166, ferredoxin hydrogenase |
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-Non-polymers , 5 types, 918 molecules
#2: Chemical | #3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.54 Å3/Da / Density % sol: 51.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Mes-NaOH (pH6), 20%PEG4000, 20% Glycerol, 0.4M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→47.48 Å / Num. obs: 126645 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 6.2627 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.78 |
Reflection shell | Resolution: 1.77→1.82 Å / Num. unique obs: 9218 / CC1/2: 0.518 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XDC Resolution: 1.77→47.48 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 36.49 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→47.48 Å
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Refine LS restraints |
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