[English] 日本語
![](img/lk-miru.gif)
- PDB-8rcc: W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8rcc | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soaked with 48 bar CO2 for 1 min | |||||||||||||||||||||||||||
![]() | (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. / Carpentier, P. / Manuel, R.R. / Pereira, I.C. / Romao, M.J. / Mota, C. | |||||||||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 264.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 197.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 59.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rc8C ![]() 8rc9C ![]() 8rcaC ![]() 8rcbC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
Experimental dataset #2 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 |
---|---|
#2: Protein | Mass: 23989.508 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 , 10 types, 142 molecules ![](data/chem/img/MGD.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/W.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/W.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SF4 / #5: Chemical | ChemComp-H2S / | #6: Chemical | ChemComp-W / | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-PEG / | #10: Chemical | ChemComp-CO2 / #11: Chemical | ChemComp-OXY / | #12: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.61 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.301→95.835 Å / Num. obs: 45048 / % possible obs: 89.19 % / Redundancy: 5.6 % / CC1/2: 0.9854 / Net I/σ(I): 6.55 |
Reflection shell | Resolution: 2.301→2.44 Å / Num. unique obs: 2252 / CC1/2: 0.465 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.536 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.301→95.835 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|