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Yorodumi- PDB-1oqv: Structure of TcpA, the Type IV pilin subunit from the toxin co-re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oqv | ||||||
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Title | Structure of TcpA, the Type IV pilin subunit from the toxin co-regulated pilus of Vibrio cholerae classical biotype | ||||||
Components | toxin-coregulated pilus subunit | ||||||
Keywords | CELL ADHESION / TcpA / Type IV pilin / pilin / pilus filament / Vibrio cholerae / fiber forming protein / adhesin / fimbriae | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Craig, L. / Tainer, J.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Type IV Pilin Structure and Assembly: X-Ray and EM Analyses of Vibrio cholerae Toxin-Coregulated Pilus and Pseudomonas aeruginosa PAK Pilin Authors: Craig, L. / Taylor, R.K. / Pique, M.E. / Adair, B.D. / Arvai, A.S. / Singh, M. / Lloyd, S.J. / Shin, D.S. / Getzoff, E.D. / Yeager, M. / Forest, K.T. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oqv.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqv.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqv ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | thousands of pilin subunits assemble to form a long thin filament 6 nm in diameter and several microns in length (see TCP model, PDB file XXX) |
-Components
#1: Protein | Mass: 19794.285 Da / Num. of mol.: 3 / Fragment: globular head domain, residues 29-199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpa / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: P23024 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 37.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, imidazole, sodium chloride, glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.975913 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2001 |
Radiation | Monochromator: single crystal Si(111) bent monochoromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975913 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 573481 / Num. obs: 115573 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.71 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 1.8 / Num. unique all: 17071 / Rsym value: 0.245 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 573481 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1.8 A structure of N-terminally truncated, SeMet-labelled TcpA Resolution: 1.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.3 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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