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Yorodumi- PDB-3phs: Crystal Structure of GBS52, the minor pilin in gram-positive path... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3phs | |||||||||
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Title | Crystal Structure of GBS52, the minor pilin in gram-positive pathogen Streptococcus agalactiae | |||||||||
Components | Cell wall surface anchor family protein | |||||||||
Keywords | Structural protein / CELL AHDESION / Ig-like fold / IgG-rev fold / GBS52 / Streptococcus agalactiae / gram-positive pilins / adhesions / CELL ADHESION / cell wall anchoring / adhesion / pilus subunit / isopeptide bond / Gram-positive bacterial cell wall | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptococcus agalactiae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.8 Å | |||||||||
Authors | Narayana, S.V.L. / Krishnan, V. | |||||||||
Citation | Journal: Structure / Year: 2007 Title: An IgG-like domain in the minor pilin GBS52 of Streptococcus agalactiae mediates lung epithelial cell adhesion. Authors: Krishnan, V. / Gaspar, A.H. / Ye, N. / Mandlik, A. / Ton-That, H. / Narayana, S.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3phs.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phs.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 3phs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3phs_validation.pdf.gz | 417.5 KB | Display | wwPDB validaton report |
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Full document | 3phs_full_validation.pdf.gz | 419.3 KB | Display | |
Data in XML | 3phs_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3phs_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phs ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phs | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 27692.242 Da / Num. of mol.: 1 / Fragment: GBS052 (unp residues 31-267) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: 2603V/R / Gene: GBS052, SAG0646 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLue / References: UniProt: Q8E0S8 |
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#2: 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: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG1500, 0.1M HEPES buffer, 0.2M Ammonium Citrate, 0.01M CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 31, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→26.81 Å / Num. all: 23655 / Num. obs: 23655 / % possible obs: 99.4 % / Redundancy: 3.01 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.33 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.6 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→26.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.643 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.941 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→26.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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