+Open data
-Basic information
Entry | Database: PDB / ID: 4m03 | ||||||
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Title | C-terminal fragment(residues 576-751) of binding region of SraP | ||||||
Components | Serine-rich adhesin for platelets | ||||||
Keywords | Calcium Binding protein / All beta / Unknown Function | ||||||
Function / homology | Function and homology information telomere maintenance / cell adhesion / calcium ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Yang, Y.H. / Jiang, Y.L. / Zhang, J. / Wang, L. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Structural Insights into SraP-Mediated Staphylococcus aureus Adhesion to Host Cells Authors: Yang, Y.H. / Jiang, Y.L. / Zhang, J. / Wang, L. / Bai, X.H. / Zhang, S.J. / Ren, Y.M. / Li, N. / Zhang, Y.H. / Zhang, Z. / Gong, Q. / Mei, Y. / Xue, T. / Zhang, J.R. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m03.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m03.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 4m03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m03 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m03 | HTTPS FTP |
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-Related structure data
Related structure data | 4m00C 4m01C 4m02SC 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: 21501.463 Da / Num. of mol.: 1 Fragment: C-terminal fragment of binding region, UNP residues 576-751 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: sraP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2FUW1 |
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#2: Chemical | ChemComp-CA / |
#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: 1.93 Å3/Da / Density % sol: 36.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M NaKPO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07138 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07138 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. all: 8890 / Num. obs: 8890 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 16.732 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 8.775 / Rsym value: 0.389 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M02 Resolution: 2.24→30.1 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.306 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 51.922 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→30.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.237→2.295 Å / Total num. of bins used: 20
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