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Yorodumi- PDB-8cja: A225L/F231A variant of the CODH/ACS complex of C. hydrogenoformans -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cja | ||||||
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Title | A225L/F231A variant of the CODH/ACS complex of C. hydrogenoformans | ||||||
Components |
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Keywords | OXIDOREDUCTASE / CODH / ACS | ||||||
Function / homology | Function and homology information 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 / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Carboxydothermus hydrogenoformans Z-2901 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ruickoldt, J. / Jeoung, J. / Lennartz, F. / Dobbek, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024 Title: Coupling CO 2 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cja.cif.gz | 573.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cja.ent.gz | 465.8 KB | Display | PDB format |
PDBx/mmJSON format | 8cja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cja_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 8cja_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 8cja_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 8cja_validation.cif.gz | 81.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/8cja ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cja | HTTPS FTP |
-Related structure data
Related structure data | 7zkvC 8cjbC 8cjcC 8cmwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Gene: ciss_06270 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1L8D0M5, anaerobic carbon monoxide dehydrogenase |
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#2: Protein | Mass: 83244.516 Da / Num. of mol.: 1 / Mutation: A225L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Gene: acsB, CHY_1222 / Production host: Escherichia coli (E. coli) References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase |
-Non-polymers , 7 types, 754 molecules
#3: Chemical | #4: Chemical | ChemComp-RQM / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ACT / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 250 g/L MPD, 40 g/L PEG 4000) were mixed with 0.28 uL 23.7 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to ...Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 250 g/L MPD, 40 g/L PEG 4000) were mixed with 0.28 uL 23.7 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to form the sitting drop. Crystallization was performed in an anoxic glove box. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 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: 1.91→48.46 Å / Num. obs: 134637 / % possible obs: 99.89 % / Redundancy: 19.8 % / CC1/2: 0.998 / Rpim(I) all: 0.071 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 19.15 % / Num. unique obs: 13158 / CC1/2: 0.205 / % possible all: 99.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.55 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 23.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.55 Å
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Refine LS restraints |
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LS refinement shell |
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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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