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Open data
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Basic information
Entry | Database: PDB / ID: 7b9a | ||||||
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Title | CooS-V with Xe-soaked | ||||||
![]() | Carbon monoxide dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Hybrid cluster / HCP / CODH | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Jeoung, J.H. / Dobbek, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold. Authors: Jeoung, J.H. / Fesseler, J. / Domnik, L. / Klemke, F. / Sinnreich, M. / Teutloff, C. / 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 | ![]() | 467.6 KB | Display | ![]() |
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PDB format | ![]() | 384.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 83.4 KB | Display | |
Data in CIF | ![]() | 112.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b7qSC ![]() 7b7tC ![]() 7b95C ![]() 7b97C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 68287.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooSV, CHY_0034 / Production host: ![]() ![]() References: UniProt: Q3AG28, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 6 types, 97 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/T2N.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/T2N.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/FES.gif)
#2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-XE / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-T2N / #6: Chemical | #7: Chemical | |
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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: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane (pH 6.5), 0.15 M KSCN and 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 PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 83046 / % possible obs: 91.6 % / Redundancy: 3.8 % / CC1/2: 0.952 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 34051 / CC1/2: 0.929 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7B7Q Resolution: 2.5→20 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.03 / 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: 196.28 Å2 / Biso mean: 26.6662 Å2 / Biso min: 5.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→20 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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