+Open data
-Basic information
Entry | Database: PDB / ID: 3v8j | ||||||
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Title | Crystal structure of Staphylococcus aureus biotin protein ligase | ||||||
Components | Biotin ligase | ||||||
Keywords | LIGASE / biotin / metabolism / biotin carboxyl carrier protein | ||||||
Function / homology | Function and homology information SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta ...SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Pendini, N.R. / Yap, M.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Selective inhibition of biotin protein ligase from Staphylococcus aureus. Authors: Soares da Costa, T.P. / Tieu, W. / Yap, M.Y. / Pendini, N.R. / Polyak, S.W. / Sejer Pedersen, D. / Morona, R. / Turnidge, J.D. / Wallace, J.C. / Wilce, M.C. / Booker, G.W. / Abell, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v8j.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v8j.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 3v8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v8j_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 3v8j_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 3v8j_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3v8j_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/3v8j ftp://data.pdbj.org/pub/pdb/validation_reports/v8/3v8j | HTTPS FTP |
-Related structure data
Related structure data | 3v7cC 3v7rC 3v7sC 3v8kC 3v8lC 4dq2C 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: 38014.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: A9781 / Gene: SAOG_00031 / Production host: Escherichia coli (E. coli) / References: UniProt: C8N5A9 |
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#2: 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: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 8000, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.51 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.51 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.96 Å |
-Processing
Software | Name: PHENIX / Version: phenix.refine: 1.8_1069 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→34.956 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 1.38 / Phase error: 27.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.54 Å2 / Biso mean: 16.7719 Å2 / Biso min: 0 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→34.956 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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