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Yorodumi- PDB-2f6r: Crystal structure of Bifunctional coenzyme A synthase (CoA syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f6r | ||||||
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Title | Crystal structure of Bifunctional coenzyme A synthase (CoA synthase): (18044849) from MUS MUSCULUS at 1.70 A resolution | ||||||
Components | Bifunctional coenzyme A synthase | ||||||
Keywords | TRANSFERASE / 18044849 / Bifunctional coenzyme A synthase (CoA synthase) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information Coenzyme A biosynthesis / dephospho-CoA kinase / dephospho-CoA kinase activity / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / mitochondrial matrix / ATP binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Bifunctional coenzyme A synthase (CoA synthase) (18044849) from MUS MUSCULUS at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f6r.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f6r.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 2f6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f6r_validation.pdf.gz | 826.3 KB | Display | wwPDB validaton report |
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Full document | 2f6r_full_validation.pdf.gz | 827.4 KB | Display | |
Data in XML | 2f6r_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 2f6r_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/2f6r ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f6r | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31448.846 Da / Num. of mol.: 1 Fragment: Phosphopantetheine adenylyltransferase and Dephospho-CoA kinase Mutation: 2.7.7.3, 2.7.1.24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Coasy, Ukr1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q9DBL7 |
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#2: Chemical | ChemComp-ACO / |
#3: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.1 Details: 15.0% iso-Propanol, 20.0% PEG-4000, 0.1M Na,K-Phosphate , pH 5.1, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→28.03 Å / Num. obs: 32283 / % possible obs: 93.2 % / Redundancy: 2.55 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.69 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.661 / Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 1n3bA Resolution: 1.7→28.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.818 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.659 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.3825 Å / Origin y: 30.5271 Å / Origin z: 25.6603 Å
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