+Open data
-Basic information
Entry | Database: PDB / ID: 4b5z | ||||||
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Title | Structure of the apo-rFnBPA(189-505) from Staphylococcus aureus | ||||||
Components | FIBRONECTIN-BINDING PROTEIN A | ||||||
Keywords | CELL ADHESION / FIBRINOGEN BINDING | ||||||
Function / homology | Function and homology information aggregation of unicellular organisms / fibrinogen binding / fibronectin binding / cell adhesion / extracellular region Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Stemberk, V. / Moroz, O. / Atkin, K.E. / Turkenburg, J.P. / Potts, J.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Evidence for Steric Regulation of Fibrinogen Binding to Staphylococcus Aureus Fibronectin-Binding Protein a (Fnbpa). Authors: Stemberk, V. / Jones, R.P. / Moroz, O. / Atkin, K.E. / Edwards, A.M. / Turkenburg, J.P. / Leech, A.P. / Massey, R.C. / Potts, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b5z.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b5z.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/4b5z ftp://data.pdbj.org/pub/pdb/validation_reports/b5/4b5z | HTTPS FTP |
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-Related structure data
Related structure data | 4b60C 1n67S 1r17S C: citing same article (ref.) S: Starting model for refinement |
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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: 35755.328 Da / Num. of mol.: 1 / Fragment: N2N3, RESIDUES 189-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14738 |
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#2: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL RESIDUES GPAM FROM VECTOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Details: PEG 20K 8%, PEG MME550 8%, 0.2 M CA AC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→56.5 Å / Num. obs: 21217 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 6 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1N67 AND 1R17 Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.469 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 189-194 AND 504-505 ARE ABSENT
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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: 32.947 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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