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Yorodumi- PDB-5h6w: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h6w | ||||||
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Title | Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain F598H mutant | ||||||
Components | Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha | ||||||
Keywords | TRANSFERASE / acetyl-Coenzyme A synthase | ||||||
Function / homology | Function and homology information CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / carbon fixation / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Moorella thermoacetica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yuan, H. | ||||||
Citation | Journal: To Be Published Title: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain F598H mutant Authors: Yuan, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h6w.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h6w.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h6w_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 5h6w_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 5h6w_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5h6w_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/5h6w ftp://data.pdbj.org/pub/pdb/validation_reports/h6/5h6w | HTTPS FTP |
-Related structure data
Related structure data | 5golC 3s2xS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14594.783 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 594-728 / Mutation: F598H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P27988, CO-methylating acetyl-CoA synthase #2: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M Citrate Sodium PH4.6, 1.6 M Sodium phosphate monobasic, 0.4 M Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Sep 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 24711 / % possible obs: 99.6 % / Redundancy: 3.3 % / Net I/σ(I): 15.76 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.56 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S2X Resolution: 2.2→43.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.39 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.427 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→43.34 Å
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Refine LS restraints |
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