+Open data
-Basic information
Entry | Database: PDB / ID: 2py0 | ||||||
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Title | Crystal structure of Cs1 pilin chimera | ||||||
Components | Fimbrial protein | ||||||
Keywords | CELL ADHESION / TYPE IV PILUS / CONSENSUS SEQUENCE / PSEUDOMONAS AERUGINOSA / MONOMERIC PILIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Kao, D.J. / Churchill, M.E. / Hodges, R.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Animal Protection and Structural Studies of a Consensus Sequence Vaccine Targeting the Receptor Binding Domain of the Type IV Pilus of Pseudomonas aeruginosa. Authors: Kao, D.J. / Churchill, M.E. / Irvin, R.T. / Hodges, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2py0.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2py0.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 2py0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/2py0 ftp://data.pdbj.org/pub/pdb/validation_reports/py/2py0 | HTTPS FTP |
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-Related structure data
Related structure data | 1dzoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12292.838 Da / Num. of mol.: 1 / Mutation: T136K, E141P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAK / Gene: pilA, fimA / Plasmid: pRLD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02973 |
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#2: Chemical | ChemComp-EPE / |
#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: 1.95 Å3/Da / Density % sol: 37.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 60% sat. Ammonium sulfate, 0.1 M HEPES., pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 21880 / Num. obs: 21824 / % possible obs: 99.73 % / Redundancy: 7.7 % / Biso Wilson estimate: 14.931 Å2 / Rsym value: 0.051 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 1.35→1.385 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 7 / Num. unique all: 2159 / Rsym value: 0.375 / % possible all: 100 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DZO, residues 25-127, backbone atoms only. Resolution: 1.35→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.899 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.934 Å2
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Refine analyze | Luzzati coordinate error obs: 0.135 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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