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Yorodumi- PDB-3st7: Crystal Structure of capsular polysaccharide assembling protein C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3st7 | ||||||
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Title | Crystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus | ||||||
Components | Capsular polysaccharide synthesis enzyme Cap5F | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / Cupid Domain / Short-Chain dehydrogenase/reductase / NADPH / UDP-4-hexulose reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å | ||||||
Authors | Miyafusa, T. / Tanaka, Y. / Kuroda, M. / Yao, M. / Watanabe, M. / Ohta, T. / Tanaka, I. / Caaveiro, J.M.M. / Tsumoto, K. | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains. Authors: Miyafusa, T. / Caaveiro, J.M. / Tanaka, Y. / Tsumoto, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Expression, purification, crystallization and preliminary diffraction analysis of CapF, a capsular polysaccharide-synthesis enzyme from Staphylococcus aureus. Authors: Miyafusa, T. / Tanaka, Y. / Kuroda, M. / Ohta, T. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3st7.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3st7.ent.gz | 133.8 KB | Display | PDB format |
PDBx/mmJSON format | 3st7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3st7_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 3st7_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 3st7_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3st7_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/3st7 ftp://data.pdbj.org/pub/pdb/validation_reports/st/3st7 | HTTPS FTP |
-Related structure data
Related structure data | 3vhrC 2zklS 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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Unit cell |
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-Components
#1: Protein | Mass: 42565.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MU50 / ATCC 700699 / Gene: capF, SAV0154 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q99X63, UniProt: A0A0H3JP37*PLUS | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Mosaicity: 0.29 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 300mM NaCl, 100mM ammonium sulfate, 100mM MES, 3.9M sodium formate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→103.52 Å / Num. all: 39695 / Num. obs: 39695 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZKL Resolution: 2.45→103.52 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2198 / WRfactor Rwork: 0.1952 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8342 / SU B: 12.193 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1641 / SU Rfree: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.2 Å2 / Biso mean: 70.4644 Å2 / Biso min: 41.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→103.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -55.1956 Å / Origin y: 12.3416 Å / Origin z: 9.6808 Å
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