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Yorodumi- PDB-6qgr: The F420-reducing [NiFe] hydrogenase complex from Methanosarcina ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qgr | ||||||
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Title | The F420-reducing [NiFe] hydrogenase complex from Methanosarcina barkeri at the Nia-S state | ||||||
Components | (Coenzyme F420 hydrogenase subunit ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / [NiFe] containing hydrogenase / reversible oxidation of dihydrogen / oxygen sensitive / methanogenic acetoclastic Archaea / METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information coenzyme F420 hydrogenase / coenzyme F420 hydrogenase activity / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding Similarity search - Function | ||||||
Biological species | Methanosarcina barkeri MS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å | ||||||
Authors | Ilina, Y. / Lorent, C. / Katz, S. / Jeoung, J.H. / Shima, S. / Horch, M. / Zebger, I. / Dobbek, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases. Authors: Ilina, Y. / Lorent, C. / Katz, S. / Jeoung, J.H. / Shima, S. / Horch, M. / Zebger, I. / Dobbek, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qgr.cif.gz | 235.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qgr.ent.gz | 180.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qgr_validation.pdf.gz | 929.9 KB | Display | wwPDB validaton report |
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Full document | 6qgr_full_validation.pdf.gz | 942.9 KB | Display | |
Data in XML | 6qgr_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 6qgr_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/6qgr ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qgr | HTTPS FTP |
-Related structure data
Related structure data | 6qgtC 6qiiC 4omfS 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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Components on special symmetry positions |
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-Components
-Coenzyme F420 hydrogenase subunit ... , 3 types, 3 molecules GAB
#1: Protein | Mass: 27598.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri MS (archaea) / References: UniProt: A0A0E3LP72, coenzyme F420 hydrogenase |
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#2: Protein | Mass: 48531.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: FRH-A harbours an active site for the dihydrogen catalysis Source: (natural) Methanosarcina barkeri MS (archaea) / References: UniProt: A0A0E3QYL7*PLUS |
#3: Protein | Mass: 32297.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri MS (archaea) / References: UniProt: A0A0E3QWH3, coenzyme F420 hydrogenase |
-Non-polymers , 10 types, 670 molecules
#4: Chemical | ChemComp-SF4 / #5: Chemical | ChemComp-FES / | #6: Chemical | #7: Chemical | ChemComp-BU3 / ( #8: Chemical | ChemComp-MPD / ( #9: Chemical | ChemComp-NFU / | #10: Chemical | ChemComp-FE / | #11: Chemical | ChemComp-MG / | #12: Chemical | ChemComp-FAD / | #13: 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: 2.48 Å3/Da / Density % sol: 50.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Tris, MPD, PEG1000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.981 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 1.839→50 Å / Num. obs: 183344 / % possible obs: 99.57 % / Redundancy: 4 % / Rrim(I) all: 0.211 / Net I/σ(I): 6.62 |
Reflection shell | Resolution: 1.8395→1.8823 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OMF Resolution: 1.839→48.138 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.78 / Phase error: 28.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.839→48.138 Å
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Refine LS restraints |
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LS refinement shell |
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