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Yorodumi- PDB-4qxz: Crystal structure of a hypothetical protein from Staphylococcus aureus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qxz | ||||||
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Title | Crystal structure of a hypothetical protein from Staphylococcus aureus | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Beta-barrel | ||||||
Function / homology | YwpF-like protein / YwpF-like protein / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å | ||||||
Authors | Lee, B.-J. / Lee, S.J. / Lee, K.-Y. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: Crystal structure of YwpF from Staphylococcus aureus reveals its architecture comprised of a beta-barrel core domain resembling type VI secretion system proteins and a two-helix pair. Authors: Lee, S.J. / Lee, K.Y. / Lee, K.Y. / Kim, D.G. / Kim, S.J. / Lee, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qxz.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qxz.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qxz_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 4qxz_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 4qxz_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4qxz_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qxz ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qxz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19328.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: Mu50 / Gene: SAV2097 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q99SG0, UniProt: A0A0H3JSS7*PLUS #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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES at pH 7.5, 25% (w/v) PEG 3350, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 12970 / % possible obs: 99.1 % |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.49→47.23 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.047 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.512 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 51.553 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→47.23 Å
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Refine LS restraints |
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