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Open data
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Basic information
Entry | Database: PDB / ID: 2y0k | ||||||
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Title | Crystal Structure of Pseudomonas Aeruginosa OpdO | ||||||
![]() | PYROGLUTATMATE PORIN OPDO | ||||||
![]() | TRANSPORT PROTEIN / OUTER MEMBRANE / TRANSPORT | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Touw, D.S. / Vijayaraghavan, J. / Vandenberg, B. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.2 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y0lC ![]() 2y0hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-C8E / ( #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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