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Yorodumi- PDB-2qx2: Structure of the C-terminal domain of sex pheromone staph-cAM373 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qx2 | ||||||
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Title | Structure of the C-terminal domain of sex pheromone staph-cAM373 precursor from Staphylococcus aureus | ||||||
Components | Sex pheromone staph-cAM373 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Staphylococcus aureus / sex pheromone staph-cAM373 precursor / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | sex pheromone staph- cam373 precursor fold / sex pheromone staph- cam373 precursor domain / CamS sex pheromone cAM373 / CamS sex pheromone cAM373 precursor / Roll / Alpha Beta / Sex pheromone staph-cAM373 / Sex pheromone staph-cAM373 Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Cuff, M.E. / Mussar, K. / Hatzos, C. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of the C-terminal domain of sex pheromone staph-cAM373 precursor from Staphylococcus aureus. Authors: Cuff, M.E. / Mussar, K. / Hatzos, C. / Gu, M. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IN UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qx2.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qx2.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qx2_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 2qx2_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 2qx2_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 2qx2_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/2qx2 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/2qx2 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39499.027 Da / Num. of mol.: 1 / Fragment: Residues 59-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Species: Staphylococcus aureus / Strain: Mu50 / Gene: CamS, SAV1903 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99SY4, UniProt: A0A0H3JSC0*PLUS | ||
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#2: Chemical | ChemComp-EDO / #3: 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: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% Ethanol, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932, 0.97943 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2006 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 29466 / Num. obs: 29466 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.2 | |||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.427 / % possible all: 57 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→34.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.069 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.143 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.548 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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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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