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Open data
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Basic information
Entry | Database: PDB / ID: 8cm5 | ||||||||||||||||||||||||||||||
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Title | W-formate dehydrogenase C872A from Desulfovibrio vulgaris | ||||||||||||||||||||||||||||||
![]() | (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. / Mota, C. / Klymanska, K. / Oliveira, A.R. / Manuel, R.R. / Pereira, I.C. / Romao, M.J. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Authors: Oliveira, A.R. / Mota, C. / Vilela-Alves, G. / Manuel, R.R. / Pedrosa, N. / Fourmond, V. / Klymanska, K. / Leger, C. / Guigliarelli, B. / Romao, M.J. / Cardoso Pereira, I.A. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 997.3 KB | Display | ![]() |
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PDB format | ![]() | 780.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cm4C ![]() 8cm6C ![]() 8cm7C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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, 8 molecules ACKRBDLS
#1: Protein | Mass: 112404.961 Da / Num. of mol.: 4 / Mutation: C872A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: fdnG-1 Production host: ![]() References: UniProt: Q72EJ1 #2: Protein | Mass: 23989.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DVU_0588 Production host: ![]() References: UniProt: Q72EJ0 |
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-Non-polymers , 7 types, 1002 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/W.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/W.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-H2S / #5: Chemical | ChemComp-W / #6: Chemical | ChemComp-MGD / #7: Chemical | ChemComp-SF4 / #8: Chemical | ChemComp-GOL / | #9: 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: 2.29 Å3/Da / Density % sol: 46.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.831 Å / Num. obs: 248226 / % possible obs: 96.8 % / Redundancy: 2.3 % / CC1/2: 0.998 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.15→2.19 Å / Num. unique obs: 12361 / CC1/2: 0.453 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.843 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→48.831 Å
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Refine LS restraints |
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LS refinement shell |
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