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Yorodumi- PDB-3hrv: Crystal structure of TcpA, a Type IV pilin from Vibrio cholerae E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hrv | ||||||
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Title | Crystal structure of TcpA, a Type IV pilin from Vibrio cholerae El Tor biotype | ||||||
Components | Toxin coregulated pilin | ||||||
Keywords | CELL ADHESION / Type IV pili / pilin / Vibrio cholerae / toxin-coregulated pilus / microcolonies / colonization / virulence factor | ||||||
Function / homology | Function and homology information extracellular organelle / protein secretion by the type II secretion system / type II protein secretion system complex / cell projection organization / pilus / : / structural molecule activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Craig, L. / Arvai, A.S. / Tainer, J.A. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2010 Title: Vibrio cholerae El Tor TcpA crystal structure and mechanism for pilus-mediated microcolony formation. Authors: Lim, M.S. / Ng, D. / Zong, Z. / Arvai, A.S. / Taylor, R.K. / Tainer, J.A. / Craig, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hrv.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hrv.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hrv_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
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Full document | 3hrv_full_validation.pdf.gz | 478.8 KB | Display | |
Data in XML | 3hrv_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 3hrv_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/3hrv ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hrv | HTTPS FTP |
-Related structure data
Related structure data | 1oqvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19742.086 Da / Num. of mol.: 2 / Fragment: globular domain, residues 29-199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor H1 / Gene: tcpA / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: Q60153 #2: Chemical | #3: Chemical | #4: 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: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na-HEPES, 1.5 M LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 7, 2003 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 23.75 / Number: 420254 / Rmerge(I) obs: 0.068 / Χ2: 1.02 / D res high: 1.5 Å / D res low: 20 Å / Num. obs: 61281 / % possible obs: 99.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.5→20 Å / Num. all: 61737 / Num. obs: 61281 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Χ2: 1.02 / Net I/σ(I): 23.746 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4.95 / Num. unique all: 6084 / Rsym value: 0.413 / Χ2: 1.078 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1OQV Resolution: 1.5→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.78 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 54.087 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.36 Å2 / Biso mean: 25.47 Å2 / Biso min: 10.28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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