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Open data
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Basic information
Entry | Database: PDB / ID: 7zxj | ||||||
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Title | K563A Mutant of Recombinant CODH-II | ||||||
![]() | Carbon monoxide dehydrogenase 2 | ||||||
![]() | OXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL / DEHYDROGENASE | ||||||
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 / peroxidase activity / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Basak, Y. / Jeoung, J.H. / Dobbek, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix Authors: Basak, Y. / Jeoung, J.H. / Domnik, L. / Ruickoldt, J. / Dobbek, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394 KB | Display | ![]() |
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PDB format | ![]() | 323.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zx3C ![]() 7zx5C ![]() 7zx6C ![]() 7zxcC ![]() 7zxlC ![]() 7zxxC ![]() 7zy1C ![]() 3b51S S: Starting model for refinement 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 66962.383 Da / Num. of mol.: 1 / Mutation: K563A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Plasmid: PLASMID / Details (production host): PET28A / Production host: ![]() ![]() References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 6 types, 928 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/WCC.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/WCC.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||
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#3: Chemical | ChemComp-FES / | ||
#4: Chemical | ChemComp-WCC / | ||
#5: Chemical | ChemComp-FE2 / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, PEG 3350 10-18%, Ammonium sulphate 0.18M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.249→40.87 Å / Num. obs: 151514 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.09 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.25→1.29 Å / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14296 / CC1/2: 0.662 / Rrim(I) all: 0.912 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3b51 Resolution: 1.249→28.01 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.77 Å2 / Biso mean: 18.0569 Å2 / Biso min: 3.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.249→28.01 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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