+Open data
-Basic information
Entry | Database: PDB / ID: 7zxc | ||||||
---|---|---|---|---|---|---|---|
Title | H96D Mutant of Recombinant CODH-II | ||||||
Components | Carbon monoxide dehydrogenase 2 | ||||||
Keywords | OXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL | ||||||
Function / homology | Function and homology information anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / nickel cation binding / generation of precursor metabolites and energy / 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: 1.696 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 | 7zxc.cif.gz | 156.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zxc.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 7zxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/7zxc ftp://data.pdbj.org/pub/pdb/validation_reports/zx/7zxc | HTTPS FTP |
---|
-Related structure data
Related structure data | 7zx3C 7zx5C 7zx6C 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: 66997.430 Da / Num. of mol.: 1 / Mutation: H96D 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 B (bacteria) / Strain (production host): ROSSETTA DE3 References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
---|
-Non-polymers , 5 types, 724 molecules
#2: Chemical | ChemComp-SF4 / |
---|---|
#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-WCC / |
#5: Chemical | ChemComp-FE / |
#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: 2.1 Å3/Da / Density % sol: 41.38 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
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: 1.696→19.874 Å / Num. obs: 61373 / % possible obs: 98.5 % / Redundancy: 4.02 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.108 / Net I/σ(I): 11.07 |
Reflection shell | Resolution: 1.696→1.72 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 2047 / CC1/2: 0.381 / Rrim(I) all: 0.378 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B51 Resolution: 1.696→19.874 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.9 / 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: 76.08 Å2 / Biso mean: 17.5634 Å2 / Biso min: 1.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.696→19.874 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|