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- PDB-5azp: Crystal structure of a membrane protein from Pseudomonas aeruginosa -
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Open data
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Basic information
Entry | Database: PDB / ID: 5azp | ||||||
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Title | Crystal structure of a membrane protein from Pseudomonas aeruginosa | ||||||
![]() | Multidrug efflux outer membrane protein OprN | ||||||
![]() | MEMBRANE PROTEIN / Alpha barrel / Beta barrel | ||||||
Function / homology | ![]() efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yonehara, R. / Yamashita, E. / Nakagawa, A. | ||||||
![]() | ![]() Title: Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa. Authors: Yonehara, R. / Yamashita, E. / Nakagawa, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 576.1 KB | Display | ![]() |
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PDB format | ![]() | 473.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5azoSC ![]() 5azsC 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 11 molecules ABC![](data/chem/img/BOG.gif)
![](data/chem/img/BOG.gif)
#1: Protein | Mass: 49686.188 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 26-472 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprN, PA2495 / Production host: ![]() ![]() #4: Sugar | ChemComp-BOG / |
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-Non-polymers , 7 types, 1931 molecules ![](data/chem/img/3PK.gif)
![](data/chem/img/OYA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OYA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-FMT / #7: Chemical | #8: Chemical | ChemComp-ACT / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.55 Å3/Da / Density % sol: 72.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 4000, sodium acetate, sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. obs: 297648 / % possible obs: 99.5 % / Redundancy: 3.6 % / Net I/σ(I): 22.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5AZO Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.816 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / 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: 26.502 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→50 Å
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Refine LS restraints |
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