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Yorodumi- PDB-3oc5: Crystal Structure of the vibrio cholerae secreted colonization fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oc5 | ||||||
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Title | Crystal Structure of the vibrio cholerae secreted colonization factor TcpF | ||||||
Components | Toxin coregulated pilus biosynthesis protein F | ||||||
Keywords | CELL ADHESION / MULTIDOMAIN PROTEIN / immunoglobulin-like (Ig-like) fold | ||||||
Function / homology | Vibrio cholerae toxin co-regulated pilus biosynthesis protein F, C-terminal domain / Vibrio cholerae toxin co-regulated pilus biosynthesis F / Vibrio cholerae toxin co-regulated pilus biosynthesis F, C-terminal / Vibrio cholerae toxin co-regulated pilus biosynthesis protein F / cell outer membrane / Immunoglobulin-like / Sandwich / Mainly Beta / Toxin coregulated pilus biosynthesis protein F Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Craig, L. / Kolappan, S. / Yuen, A.S.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal Structure of the Vibrio cholerae Colonization Factor TcpF and Identification of a Functional Immunogenic Site. Authors: Megli, C.J. / Yuen, A.S. / Kolappan, S. / Richardson, M.R. / Dharmasena, M.N. / Krebs, S.J. / Taylor, R.K. / Craig, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oc5.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oc5.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3oc5 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3oc5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35882.938 Da / Num. of mol.: 1 / Fragment: UNP residues 21-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpF, VC_0837 / Production host: Vibrio cholerae (bacteria) / References: UniProt: P0C6Q5 |
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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: 3.3 Å3/Da / Density % sol: 62.74 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: (NH4)2 H PO4 1M, Imidazole 100 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9116,0.9794 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2007 | |||||||||
Radiation | Monochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→20 Å / Num. obs: 19524 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→19.65 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.281 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R Free: 0.22 / 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: 58.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 59.423 Å / Origin y: -38.2792 Å / Origin z: -15.7493 Å
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