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Yorodumi- PDB-4f24: Crystal structures reveal the multi-ligand binding mechanism of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f24 | ||||||
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Title | Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB | ||||||
Components | Clumping factor B | ||||||
Keywords | CELL ADHESION / Dev-IgG fold / CK10 / cell surface | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.509 Å | ||||||
Authors | Yang, M.J. / Xiang, H. / Wang, J.W. / Liu, B. / Chen, Y.G. / Liu, L. / Deng, X.M. / Feng, Y. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus aureus ClfB Authors: Xiang, H. / Feng, Y. / Wang, J.W. / Liu, B. / Chen, Y.G. / Liu, L. / Deng, X.M. / Yang, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f24.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f24.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 4f24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f24_validation.pdf.gz | 428.4 KB | Display | wwPDB validaton report |
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Full document | 4f24_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 4f24_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4f24_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/4f24 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/4f24 | HTTPS FTP |
-Related structure data
Related structure data | 4f1zC 4f20C 4f27SC 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: 39875.512 Da / Num. of mol.: 1 / Fragment: UNP residues 197-542 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: clfB, SAR2709 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GDH2 |
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#2: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M LiSO4, 0.1M Tris-HCl pH8.5, 30% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2011 | ||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.509→47.211 Å / Num. all: 13816 / Num. obs: 13816 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.11 Å2 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4F27 Resolution: 2.509→42.227 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 0 / Phase error: 28.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.951 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 188.64 Å2 / Biso mean: 76.1017 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.509→42.227 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: 5
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Refinement TLS params. | Method: refined / Origin x: 26.914 Å / Origin y: -13.0685 Å / Origin z: 9.3452 Å
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Refinement TLS group | Selection details: chain A |