+Open data
-Basic information
Entry | Database: PDB / ID: 7zx3 | ||||||
---|---|---|---|---|---|---|---|
Title | C295D Mutant of Recombinant CODH-II | ||||||
Components | Carbon monoxide dehydrogenase 2 | ||||||
Keywords | OXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL / DEHYDROGENASE | ||||||
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 / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Carboxydothermus hydrogenoformans Z-2901 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å | ||||||
Authors | Basak, Y. / Jeoung, J.H. / Dobbek, H. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Acs Catalysis / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7zx3.cif.gz | 249.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zx3.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/7zx3 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/7zx3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7zx5C 7zx6C 7zxcC 7zxjC 7zxlC 7zxxC 7zy1C 3b51S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 67032.430 Da / Num. of mol.: 1 / Mutation: C295D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSSETTA DE3 References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
---|
-Non-polymers , 5 types, 439 molecules
#2: Chemical | #3: Chemical | ChemComp-FES / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: 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: 2.09 Å3/Da / Density % sol: 41.08 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→40.78 Å / Num. obs: 61984 / % possible obs: 99.2 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.072 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 4.09 % / Num. unique obs: 6106 / CC1/2: 0.769 / % possible all: 98.26 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3b51 Resolution: 1.683→37.525 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.61 / 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: 109.81 Å2 / Biso mean: 27.1319 Å2 / Biso min: 10.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.683→37.525 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|