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Yorodumi- PDB-6ttl: crystal structure of [FeFe]-hydrogenase CbA5H (partial) from Clos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ttl | ||||||
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Title | crystal structure of [FeFe]-hydrogenase CbA5H (partial) from Clostridium beijerinckii in Hinact state | ||||||
Components | [FeFe]-hydrogenase | ||||||
Keywords | OXIDOREDUCTASE / [FeFe]-hydrogenase / aerobically crystallized / Clostridium beijerinckii | ||||||
Function / homology | Function and homology information ferredoxin hydrogenase activity / iron-sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Clostridium beijerinckii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Duan, J. / Rutz, A. / Hofmann, E. / Happe, T. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: A safety cap protects hydrogenase from oxygen attack. Authors: Winkler, M. / Duan, J. / Rutz, A. / Felbek, C. / Scholtysek, L. / Lampret, O. / Jaenecke, J. / Apfel, U.P. / Gilardi, G. / Valetti, F. / Fourmond, V. / Hofmann, E. / Leger, C. / Happe, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ttl.cif.gz | 206.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ttl.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ttl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/6ttl ftp://data.pdbj.org/pub/pdb/validation_reports/tt/6ttl | HTTPS FTP |
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-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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Unit cell |
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-Components
#1: Protein | Mass: 75001.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): delta iscR / References: UniProt: A0A1I9RYV3 #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
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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: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 0.4M MgCl2, 27% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 2, 2018 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976247 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.26 Å / Num. obs: 41295 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 87.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.36 |
Reflection shell | Resolution: 2.9→2.98 Å / Num. unique obs: 3028 / CC1/2: 0.477 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XDC Resolution: 2.9→49.26 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 71.68 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.26 Å
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Refine LS restraints |
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