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Yorodumi- PDB-5gol: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gol | ||||||
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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 / SAD / Resolution: 2.11 Å | ||||||
Authors | Yuan, H. / Wei, Y.Z. / Tan, X.S. | ||||||
Citation | Journal: To Be Published Title: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain F598H mutant Authors: Yuan, H. / Wei, Y.Z. / Tan, X.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gol.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gol.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 5gol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gol_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 5gol_full_validation.pdf.gz | 464.2 KB | Display | |
Data in XML | 5gol_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 5gol_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/5gol ftp://data.pdbj.org/pub/pdb/validation_reports/go/5gol | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 14594.783 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 598-728 / 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: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NI / #4: 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: 2.56 Å3/Da / Density % sol: 52.03 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MES PH 7.0 0.1M, 1.6M Ammonia Sulfate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.48 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.48 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 34491 / % possible obs: 99.7 % / Redundancy: 7.4 % / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 7.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.11→31.24 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.386 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.192 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. 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: 34.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→31.24 Å
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Refine LS restraints |
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