+Open data
-Basic information
Entry | Database: PDB / ID: 2y0k | ||||||
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Title | Crystal Structure of Pseudomonas Aeruginosa OpdO | ||||||
Components | PYROGLUTATMATE PORIN OPDO | ||||||
Keywords | TRANSPORT PROTEIN / OUTER MEMBRANE / TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å | ||||||
Authors | Touw, D.S. / Vijayaraghavan, J. / Vandenberg, B. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Pseudomonas Aeruginosa Opdo Authors: Touw, D.S. / Vijayaraghavan, J. / Vandenberg, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y0k.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y0k.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 2y0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y0k_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 2y0k_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 2y0k_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 2y0k_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/2y0k ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y0k | HTTPS FTP |
-Related structure data
Related structure data | 2y0lC 2y0hS S: Starting model for refinement C: citing same article (ref.) |
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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: 42683.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PB22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I202 | ||
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#2: Chemical | ChemComp-C8E / ( #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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM ACETATE PH 5.5, 8.8% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 26233 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 31.13 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y0H Resolution: 2.295→19.747 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 23.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.096 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.295→19.747 Å
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Refine LS restraints |
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LS refinement shell |
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