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Yorodumi- PDB-6yu9: CO-dehydrogenase homodimer from Clostridium autoethanogenum at 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yu9 | |||||||||
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Title | CO-dehydrogenase homodimer from Clostridium autoethanogenum at 1.90-A resolution | |||||||||
Components | Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor) | |||||||||
Keywords | OXIDOREDUCTASE / C1-Metabolism / Carbon monoxide / metallo-containing protein / Acetogenic bacteria / Acetogenesis / CO-dehydrogenase/Acetyl-CoA synthase / X-ray crystal structure / Gas channeling / Waste-gas conversion | |||||||||
Function / homology | Function and homology information carbon-monoxide dehydrogenase (acceptor) / : / nickel cation binding / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding Similarity search - Function | |||||||||
Biological species | Clostridium autoethanogenum DSM 10061 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å | |||||||||
Authors | Wagner, T. / Lemaire, O.N. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2020 Title: Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum. Authors: Lemaire, O.N. / Wagner, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yu9.cif.gz | 946 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yu9.ent.gz | 786 KB | Display | PDB format |
PDBx/mmJSON format | 6yu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yu9_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
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Full document | 6yu9_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 6yu9_validation.xml.gz | 90 KB | Display | |
Data in CIF | 6yu9_validation.cif.gz | 132 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yu9 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yu9 | HTTPS FTP |
-Related structure data
Related structure data | 6yttSC 6yuaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 67977.531 Da / Num. of mol.: 4 / Mutation: Wild-type / Source method: isolated from a natural source Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401). ...Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).,A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401). Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria) Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: / References: UniProt: U5RTE2, carbon-monoxide dehydrogenase (acceptor) |
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-Non-polymers , 6 types, 1125 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-XCC / #5: Chemical | #6: Chemical | ChemComp-CL / | #7: 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: 2.56 Å3/Da / Density % sol: 52.05 % / Description: Brownish thick quadratic plates |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96- ...Details: Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96-well MRC 2 Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 uL of mother liquor, crystallization drop contained a mixture of 0.6 uL protein and 0.6 uL precipitant. The protein concentration was 16.9 mg/mL in 25 mM Tris/HCl pH7.6, 10% glycerol (v/v) and 2 mM dithiothreitol. The best diffracting crystal of CODH was obtained by initial screening using the Shotgun (SG1) screen from Molecular dimensions. The crystallization reservoir contained 200 mM Magnesium acetate tetrahydrate; 20% (w/v) polyethylene glycol 3350. Crystals were cryo protected in the same solution supplemented with 25% glycerol (v/v). Temp details: Fluctuation of 1 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→119.4 Å / Num. obs: 102786 / % possible obs: 93.3 % / Redundancy: 6.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.088 / Rrim(I) all: 0.223 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.9→2.179 Å / Redundancy: 4 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5140 / CC1/2: 0.611 / Rpim(I) all: 0.45 / Rrim(I) all: 0.928 / % possible all: 63.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YTT Resolution: 1.904→49.75 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.372 / SU Rfree Blow DPI: 0.216
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Displacement parameters | Biso max: 136.93 Å2 / Biso mean: 33.12 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.904→49.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.904→2.07 Å / 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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