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Yorodumi- PDB-4m00: Crystal structure of the ligand binding region of staphylococcal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m00 | |||||||||
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Title | Crystal structure of the ligand binding region of staphylococcal adhesion 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 4m00.cif.gz | 125.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m00.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 4m00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m00_validation.pdf.gz | 908.3 KB | Display | wwPDB validaton report |
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Full document | 4m00_full_validation.pdf.gz | 910.3 KB | Display | |
Data in XML | 4m00_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 4m00_validation.cif.gz | 40.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m00 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m00 | HTTPS FTP |
-Related structure data
Related structure data | 4m01SC 4m02C 4m03C S: Starting model for refinement 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: 56361.020 Da / Num. of mol.: 1 / Fragment: ligand binding region, UNP residues 245-751 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: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose | ||||
#3: Chemical | #4: Chemical | ChemComp-MES / | #5: 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: 4.87 Å3/Da / Density % sol: 74.72 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.8M ammonium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2013 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 69226 / Num. obs: 69226 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 5.754 / Num. unique all: 475054 / Rsym value: 0.385 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M01 Resolution: 2.05→41.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.558 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / 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: 29.548 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→41.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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