+Open data
-Basic information
Entry | Database: PDB / ID: 1oqw | ||||||
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Title | Full-Length PAK Pilin from Pseudomonas aeruginosa | ||||||
Components | Fimbrial protein | ||||||
Keywords | CELL ADHESION / Type IV pilin / fiber-forming protein / adhesion / Pseudomonas aerugionosa / PAK pilin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Craig, L. / Arvai, A.S. / Forest, K.T. / 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.A. / 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 | 1oqw.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqw.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqw ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqw | HTTPS FTP |
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-Related structure data
Related structure data | 1oqvC 1dzoS C: citing same article (ref.) 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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2 |
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Unit cell |
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Details | thousands of pilin subunits assemble to form a long thin filament ~8 nm in diameter and several microns in length |
-Components
#1: Protein | Mass: 15021.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: K / References: UniProt: P02973 #2: 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: 3.21 Å3/Da / Density % sol: 61.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 15% MPD, 35% PEG 4000, 100 mM sodium citrate, 2.5 mM MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING 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: BL9-2 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 29079 / Num. obs: 28468 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.24 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.28 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2875 / % possible all: 83.6 |
Reflection | *PLUS Num. obs: 29308 / Num. measured all: 324152 |
Reflection shell | *PLUS % possible obs: 83.6 % / Rmerge(I) obs: 0.329 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DZO.pdb Resolution: 2→30 Å / Cross valid method: used throughout refinement / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.3 Å /
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.007 |