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Yorodumi- PDB-3tw0: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tw0 | ||||||
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Title | Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae | ||||||
Components | Cell wall surface anchor family protein | ||||||
Keywords | CELL ADHESION / vWFA fold / Ancillary pilin / Gram-positive bacterial cell surface | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae serogroup V (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Krishnan, V. / Narayana, S.V.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions. Authors: Krishnan, V. / Dwivedi, P. / Kim, B.J. / Samal, A. / Macon, K. / Ma, X. / Mishra, A. / Doran, K.S. / 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 | 3tw0.cif.gz | 304.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tw0.ent.gz | 245.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/3tw0 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/3tw0 | HTTPS FTP |
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-Related structure data
Related structure data | 3tvySC 3txaC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41639.133 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / Mutation: T564C, K571C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria) Strain: 2603 V/R / Gene: SAG0649 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8E0S5 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Sequence details | N3 DOMAIN (UNP RESIDUES 212-581) REMAINS AFTER DEGRADATION OF ORIGINAL PROTEIN CONSTRUCT (UNP ...N3 DOMAIN (UNP RESIDUES 212-581) REMAINS AFTER DEGRADATIO | |
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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: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3000, 0.1 M HEPES, 0.2 M NaCl, 10 mM Spermine-4HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: Apr 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.304 Å / Num. obs: 88454 / % possible obs: 89 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.2 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TVY Resolution: 2→46.304 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.843 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 24.932 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.304 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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