+Open data
-Basic information
Entry | Database: PDB / ID: 8rcg | |||||||||||||||||||||||||||
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Title | W-formate dehydrogenase M405S from Desulfovibrio vulgaris | |||||||||||||||||||||||||||
Components | (Formate dehydrogenase, ...) x 2 | |||||||||||||||||||||||||||
Keywords | OXIDOREDUCTASE / Formate / CO2 / Molybdenum and Tungsten enzymes / DMSO reductase family / ELECTRON TRANSPORT | |||||||||||||||||||||||||||
Function / homology | Function and homology information formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / cellular respiration / molybdopterin cofactor binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å | |||||||||||||||||||||||||||
Authors | Vilela-Alves, G. / Manuel, R.R. / Pereira, I.C. / Romao, M.J. / Mota, C. | |||||||||||||||||||||||||||
Funding support | Portugal, 8items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2024 Title: Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. Authors: Vilela-Alves, G. / Rebelo Manuel, R. / Pedrosa, N. / Cardoso Pereira, I.A. / Romao, M.J. / Mota, C. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rcg.cif.gz | 266.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rcg.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 8rcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/8rcg ftp://data.pdbj.org/pub/pdb/validation_reports/rc/8rcg | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Experimental dataset #1 | Data reference: 10.15151/ESRF-ES-1019005467 / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.51093/xrd-00184 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Formate dehydrogenase, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 112392.906 Da / Num. of mol.: 1 / Mutation: M405S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria) Strain: Hildenborough / Gene: fdnG-1 Production host: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria) Strain (production host): Hildenborough / References: UniProt: Q72EJ1 |
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#2: Protein | Mass: 23989.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria) Strain: Hildenborough / Gene: DVU_0588 Production host: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria) Strain (production host): Hildenborough / References: UniProt: Q72EJ0 |
-Non-polymers , 8 types, 258 molecules
#3: Chemical | #4: Chemical | ChemComp-SF4 / #5: Chemical | ChemComp-H2S / | #6: Chemical | ChemComp-W / | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-PEG / | #9: Chemical | ChemComp-EDO / | #10: Water | ChemComp-HOH / | |
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-Details
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: 2.22 Å3/Da / Density % sol: 44.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 32% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.005→48.592 Å / Num. obs: 71441 / % possible obs: 93.02 % / Redundancy: 4.61 % / CC1/2: 0.996 / Net I/σ(I): 7.381 |
Reflection shell | Resolution: 2.005→2.118 Å / Num. unique obs: 3573 / CC1/2: 0.562 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→48.592 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.12 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.203 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.166 Å2
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Refinement step | Cycle: LAST / Resolution: 2.005→48.592 Å
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Refine LS restraints |
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LS refinement shell |
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