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Open data
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Basic information
Entry | Database: PDB / ID: 7zkv | ||||||
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Title | F231A variant of the CODH/ACS complex of C. hydrogenoformans | ||||||
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![]() | OXIDOREDUCTASE / CO2 reduction / acetyl-CoA synthesis / carbon monoxide | ||||||
Function / homology | ![]() CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity ...CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruickoldt, J. / Jeoung, J.-H. / Basak, Y. / Domnik, L. / Dobbek, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Coupling CO2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis. Authors: Ruickoldt, J. / Jeoung, J.H. / Rudolph, M.A. / Lennartz, F. / Kreibich, J. / Schomacker, R. / Dobbek, H. #1: ![]() Title: On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases Authors: Ruickoldt, J. / Basak, Y. / Domnik, L. / Jeoung, J.H. / 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 | ![]() | 583.4 KB | Display | ![]() |
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PDB format | ![]() | 472.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cjaC ![]() 8cjbC ![]() 8cjcC ![]() 7zkjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 73096.000 Da / Num. of mol.: 1 / Mutation: F231A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ciss_06270 / Production host: ![]() ![]() References: UniProt: A0A1L8D0M5, anaerobic carbon monoxide dehydrogenase |
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#2: Protein | Mass: 82111.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: acsB, CHY_1222 / Production host: ![]() ![]() References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase |
-Non-polymers , 8 types, 981 molecules ![](data/chem/img/RQM.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-RQM / | ||||||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Chemical | ChemComp-NA / | #10: 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: 2.76 Å3/Da / Density % sol: 55.37 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: To form the drops 0.7 uL of the reservoir solution (0.1 M Na-acetate pH 5, 40 g/L PEG 4000, 210 g/L MPD) were mixed with 0.7 uL of 29.6 g/L CODH/ACS solution in 50 mM Mops pH 7.6, 150 mM ...Details: To form the drops 0.7 uL of the reservoir solution (0.1 M Na-acetate pH 5, 40 g/L PEG 4000, 210 g/L MPD) were mixed with 0.7 uL of 29.6 g/L CODH/ACS solution in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA |
-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: Jun 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.066→48.55 Å / Num. obs: 106961 / % possible obs: 99.73 % / Redundancy: 39.82 % / CC1/2: 0.998 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.07→2.14 Å / Num. unique obs: 10238 / CC1/2: 0.512 / % possible all: 97.32 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ZKJ Resolution: 2.066→42.382 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.64 / 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: 102.13 Å2 / Biso mean: 38.9564 Å2 / Biso min: 18.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.066→42.382 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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