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Yorodumi- PDB-2vq2: Crystal structure of PilW, widely conserved type IV pilus biogene... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vq2 | ||||||
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Title | Crystal structure of PilW, widely conserved type IV pilus biogenesis factor | ||||||
Components | PUTATIVE FIMBRIAL BIOGENESIS AND TWITCHING MOTILITY PROTEIN | ||||||
Keywords | STRUCTURAL PROTEIN / SECRETIN / TPR REPEAT / TYPE IV PILUS / BACTERAIL VIRULENCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.54 Å | ||||||
Authors | Trinidade, M.B. / Job, V. / Contreras-Martel, C. / Pelicic, V. / Dessen, A. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2008 Title: Structure of a widely conserved type IV pilus biogenesis factor that affects the stability of secretin multimers. Authors: Trindade, M.B. / Job, V. / Contreras-Martel, C. / Pelicic, V. / Dessen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vq2.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vq2.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vq2 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vq2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25375.605 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Plasmid: PMAL-P2X / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9JZ41 |
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-Non-polymers , 6 types, 327 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | ChemComp-GOL / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO3 / | #6: Chemical | ChemComp-MG / | #7: 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: 2.47 Å3/Da / Density % sol: 50.15 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING-DROP VAPOR DIFFUSION METHOD, 20C 100MM TRIS HCL PH8.5, 800MM LI2SO4, 10MM NICL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. obs: 71188 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 23.15 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37 |
Reflection shell | Resolution: 1.54→1.63 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 7.1 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 1.54→75.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.125 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.071 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→75.81 Å
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Refine LS restraints |
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