+Open data
-Basic information
Entry | Database: PDB / ID: 4m01 | ||||||
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Title | N terminal fragment(residues 245-575) of binding region of SraP | ||||||
Components | Serine-rich adhesin for platelets | ||||||
Keywords | CELL ADHESION / All beta / Adhesion / Carbohydrate/Sugar Binding | ||||||
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 / SAD / Resolution: 2.1 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 | 4m01.cif.gz | 277.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m01.ent.gz | 231 KB | Display | PDB format |
PDBx/mmJSON format | 4m01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m01_validation.pdf.gz | 466.1 KB | Display | wwPDB validaton report |
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Full document | 4m01_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 4m01_validation.xml.gz | 58.5 KB | Display | |
Data in CIF | 4m01_validation.cif.gz | 89.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m01 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m01 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38805.848 Da / Num. of mol.: 4 Fragment: N-terminal fragment of binding region, UNP residues 245-575 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 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: 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: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% PEG 6000, 0.1M MES, 1.0M lithium chloride, pH 6.0, 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: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 99475 / Num. obs: 99475 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 21.37 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.158 / Net I/σ(I): 14.346 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5.63 / Num. unique all: 686821 / Rsym value: 0.357 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.911 Å / Occupancy max: 1 / Occupancy min: 0.75 / FOM work R set: 0.8685 / SU ML: 0.5 / σ(F): 1.38 / Phase error: 20.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.466 Å2 / ksol: 0.333 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.31 Å2 / Biso mean: 24.1404 Å2 / Biso min: 8.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.911 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: 30
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