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Yorodumi- PDB-4omf: The F420-reducing [NiFe]-hydrogenase complex from Methanothermoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4omf | ||||||
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Title | The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member | ||||||
Components | (F420-reducing hydrogenase, subunit ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / [NiFe]-center / 3[4Fe-4S] cluster / ferredoxin fold / FAD binding / potential F420 binding / anaerobic enzyme | ||||||
Function / homology | Function and homology information coenzyme F420 hydrogenase / coenzyme F420 hydrogenase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding Similarity search - Function | ||||||
Biological species | Methanothermobacter marburgensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / cryo-EM model of FrhABG complex, calculated SAD phases were combined / Resolution: 1.71 Å | ||||||
Authors | Vitt, S. / Ma, K. / Warkentin, E. / Moll, J. / Pierik, A. / Shima, S. / Ermler, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. Authors: Vitt, S. / Ma, K. / Warkentin, E. / Moll, J. / Pierik, A.J. / Shima, S. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4omf.cif.gz | 374.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4omf.ent.gz | 300.5 KB | Display | PDB format |
PDBx/mmJSON format | 4omf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4omf_validation.pdf.gz | 888.4 KB | Display | wwPDB validaton report |
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Full document | 4omf_full_validation.pdf.gz | 893.1 KB | Display | |
Data in XML | 4omf_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 4omf_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/4omf ftp://data.pdbj.org/pub/pdb/validation_reports/om/4omf | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-F420-reducing hydrogenase, subunit ... , 3 types, 3 molecules GAB
#1: Protein | Mass: 30267.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / References: UniProt: D9PYF7, coenzyme F420 hydrogenase |
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#2: Protein | Mass: 44873.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / References: UniProt: D9PYF9, coenzyme F420 hydrogenase |
#3: Protein | Mass: 30778.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / References: UniProt: D9PYF6, coenzyme F420 hydrogenase |
-Non-polymers , 10 types, 776 molecules
#4: Chemical | ChemComp-SF4 / #5: Chemical | ChemComp-DTZ / | #6: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-NFU / | #9: Chemical | ChemComp-CL / | #10: Chemical | ChemComp-KEN / | #11: Chemical | ChemComp-UNK / | #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: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 17-20 % PEE797, 100 mM MES/NaOH, 400 mM MgCl2, 5% glycerol, 100 mM trimethylamine oxide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0, 1.71 | |||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2011 | |||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. obs: 112689 / % possible obs: 86.1 % / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: cryo-EM model of FrhABG complex, calculated SAD phases were combined Resolution: 1.71→19.99 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→19.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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