+Open data
-Basic information
Entry | Database: PDB / ID: 7b7q | ||||||
---|---|---|---|---|---|---|---|
Title | CooS-V with oxidized hybrid cluster | ||||||
Components | Carbon monoxide dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Hybrid cluster / HCP / CODH | ||||||
Function / homology | Function and homology information 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 | Carboxydothermus hydrogenoformans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Jeoung, J.H. / Dobbek, H. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7b7q.cif.gz | 735.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7b7q.ent.gz | 615.6 KB | Display | PDB format |
PDBx/mmJSON format | 7b7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b7q_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7b7q_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7b7q_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 7b7q_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/7b7q ftp://data.pdbj.org/pub/pdb/validation_reports/b7/7b7q | HTTPS FTP |
-Related structure data
Related structure data | 7b7tC 7b95C 7b97C 7b9aC 3b53S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 68319.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CSS is S-MERCAPTOCYSTEINE. Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria) Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooSV, CHY_0034 / Production host: Escherichia coli (E. coli) References: UniProt: Q3AG28, anaerobic carbon monoxide dehydrogenase |
---|
-Non-polymers , 6 types, 1294 molecules
#2: Chemical | ChemComp-FES / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TAM / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.2 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
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: 1.35→45.362 Å / Num. obs: 251838 / % possible obs: 99.06 % / Redundancy: 5.1 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.35→1.4 Å / Num. unique obs: 251838 / CC1/2: 0.999 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B53 Resolution: 1.35→45.362 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.25 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.66 Å2 / Biso mean: 26.4203 Å2 / Biso min: 12.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→45.362 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|