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Open data
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Basic information
Entry | Database: PDB / ID: 7b97 | ||||||
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Title | CooS-V with oxidized hybrid cluster by hydroxylamine for 30 min | ||||||
![]() | 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 | ![]() | 719.7 KB | Display | ![]() |
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PDB format | ![]() | 603.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 84.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b7qSC ![]() 7b7tC ![]() 7b95C ![]() 7b9aC 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: 68287.820 Da / Num. of mol.: 2 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, 1150 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/T2N.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/BU3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/T2N.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/BU3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FES / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-BU3 / ( #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: 2.11 Å3/Da / Density % sol: 41.82 % |
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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: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→48.752 Å / Num. obs: 194715 / % possible obs: 97.19 % / Redundancy: 6.9 % / CC1/2: 1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.45→1.51 Å / Num. unique obs: 45085 / CC1/2: 0.77 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7B7Q Resolution: 1.45→48.752 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.52 / 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: 93.58 Å2 / Biso mean: 26.9294 Å2 / Biso min: 11.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→48.752 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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