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- PDB-8rcb: W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystall... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rcb | |||||||||||||||||||||||||||
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Title | W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air (in a not degassed drop) for 34 min in the presence of Formate | |||||||||||||||||||||||||||
![]() | (Formate dehydrogenase, ...) x 2 | |||||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / Formate / CO2 / Molybdenum and Tungsten enzymes / DMSO reductase family / ELECTRON TRANSPORT | |||||||||||||||||||||||||||
Function / homology | ![]() formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Vilela-Alves, G. / Manuel, R.R. / Pereira, I.C. / Romao, M.J. / Mota, C. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement Authors: Vilela-Alves, G. / Manuel, R.R. / Viegas, A. / Carpentier, P. / Biaso, F. / Guigliarelli, B. / Pereira, I.C. / Romao, M.J. / Mota, C. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262 KB | Display | ![]() |
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PDB format | ![]() | 196 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rc8C ![]() 8rc9C ![]() 8rcaC ![]() 8rccC ![]() 6sdvS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
Experimental dataset #2 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Formate dehydrogenase, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 112437.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Hildenborough / Gene: fdnG-1, DVU_0587 Production host: ![]() Strain (production host): Hildenborough / References: UniProt: Q72EJ1, formate dehydrogenase |
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#2: Protein | Mass: 23858.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Hildenborough / Gene: DVU_0588 Production host: ![]() Strain (production host): Hildenborough / References: UniProt: Q72EJ0 |
-Non-polymers , 9 types, 108 molecules ![](data/chem/img/MGD.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/W.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/W.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SF4 / #5: Chemical | ChemComp-W / | #6: Chemical | ChemComp-H2S / | #7: Chemical | #8: Chemical | ChemComp-PEG / | #9: Chemical | #10: Chemical | ChemComp-OXY / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 24% 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→94.67 Å / Num. obs: 54097 / % possible obs: 91.15 % / Redundancy: 8.9 % / CC1/2: 0.996 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.11→2.28 Å / Num. unique obs: 2705 / CC1/2: 0.591 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SDV Resolution: 2.11→94.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.753 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R: 0.383 / ESU R Free: 0.239 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: 1.1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.678 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→94.67 Å
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Refine LS restraints |
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LS refinement shell |
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