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Yorodumi- PDB-6gm7: [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E144A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gm7 | ||||||
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Title | [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E144A | ||||||
Components | Fe-hydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Hydrogenase / H-cluster / apo-form | ||||||
Function / homology | Function and homology information 1.18.99.1 / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å | ||||||
Authors | Duan, J. / Engelbrecht, V. / Esselborn, J. / Hofmann, E. / Winkler, M. / Happe, T. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases. Authors: Duan, J. / Senger, M. / Esselborn, J. / Engelbrecht, V. / Wittkamp, F. / Apfel, U.P. / Hofmann, E. / Stripp, S.T. / Happe, T. / Winkler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gm7.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gm7.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/6gm7 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/6gm7 | HTTPS FTP |
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-Related structure data
Related structure data | 6glyC 6glzC 6gm0C 6gm1C 6gm2C 6gm3C 6gm4C 6gm5C 6gm6C 6gm8C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48819.684 Da / Num. of mol.: 1 / Fragment: apo enzyme / Mutation: E144A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) Gene: hyd1, HYD1, hydA, hydA1, CHLRE_03g199800v5, CHLREDRAFT_183963 Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DiscR / References: UniProt: Q9FYU1, 1.18.99.1 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 4000, 0.4 M NaCl,0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 26, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→48.1195 Å / Num. obs: 25469 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.165 / Rsym value: 0.179 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.14→48.107 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.68 Å2 / Biso mean: 30.1692 Å2 / Biso min: 11.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.14→48.107 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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