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- PDB-6vwy: Crystal structure of C45G/T50C D. vulgaris carbon monoxide dehydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vwy | |||||||||||||||
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Title | Crystal structure of C45G/T50C D. vulgaris carbon monoxide dehydrogenase (anaerobic) | |||||||||||||||
![]() | Carbon monoxide dehydrogenase | |||||||||||||||
![]() | OXIDOREDUCTASE / nickel-iron-sulfur (Ni-Fe-S) cluster / iron-sulfur (Fe-S) cluster / metalloenzyme | |||||||||||||||
Function / homology | ![]() anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / peroxidase activity / 4 iron, 4 sulfur cluster binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Wittenborn, E.C. / Drennan, C.L. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance inDesulfovibrio vulgarisNi-Fe Carbon Monoxide Dehydrogenase. Authors: Wittenborn, E.C. / Guendon, C. / Merrouch, M. / Benvenuti, M. / Fourmond, V. / Leger, C. / Drennan, C.L. / Dementin, S. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 491.8 KB | Display | ![]() |
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PDB format | ![]() | 400.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 374.4 KB | Display | ![]() |
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Full document | ![]() | 374.3 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vwzC ![]() 6vx0C ![]() 6vx1C ![]() 6b6vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 66706.711 Da / Num. of mol.: 2 / Mutation: C45G/T50C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: cooS, DVU_2098 / Production host: ![]() References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 5 types, 815 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/XCC.gif)
![](data/chem/img/CUV.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/XCC.gif)
![](data/chem/img/CUV.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 2.24 Å3/Da / Density % sol: 44.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 150-250 mM magnesium chloride, 16-20% w/v PEG3350 |
-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: Apr 8, 2016 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→100 Å / Num. obs: 102654 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.83→1.87 Å / Num. unique obs: 7601 / CC1/2: 0.829 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6B6V Resolution: 1.83→73.68 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.71 Å2 / Biso mean: 29.9732 Å2 / Biso min: 15.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→73.68 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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