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Yorodumi- PDB-3jyz: Crystal structure of Pseudomonas aeruginosa (strain: Pa110594) ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jyz | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa (strain: Pa110594) typeIV pilin in space group P41212 | ||||||
Components | Type IV pilin structural subunit | ||||||
Keywords | STRUCTURAL PROTEIN / PilA / Methylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Nguyen, Y. / Jackson, S.G. / Aidoo, F. / Junop, M.S. / Burrows, L.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural characterization of Novel Pseudomonas aeruginosa type IV pilins. Authors: Nguyen, Y. / Jackson, S.G. / Aidoo, F. / Junop, M. / Burrows, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jyz.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jyz.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 3jyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/3jyz ftp://data.pdbj.org/pub/pdb/validation_reports/jy/3jyz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15439.632 Da / Num. of mol.: 1 / Fragment: UNP residues 34-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA110594 / Gene: pilA / Plasmid: D-TOPO-pET151 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KQ36 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2009 / Details: beam focused by a toroidal mirror |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 20404 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 33.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→29.8424 Å / SU ML: 0.2 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.96 Å2 / ksol: 0.356 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→29.8424 Å
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Refine LS restraints |
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LS refinement shell |
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