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Open data
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Basic information
Entry | Database: PDB / ID: 3syb | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa OccD3 (OpdP) | ||||||
![]() | Glycine-glutamate dipeptide porin OpdP | ||||||
![]() | MEMBRANE PROTEIN / beta-barrel / channel / bacterial outer membrane | ||||||
Function / homology | ![]() dipeptide transmembrane transporter activity / channel activity / porin activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | van den Berg, B. / Eren, E. | ||||||
![]() | ![]() Title: Substrate Specificity within a Family of Outer Membrane Carboxylate Channels. Authors: Eren, E. / Vijayaraghavan, J. / Liu, J. / Cheneke, B.R. / Touw, D.S. / Lepore, B.W. / Indic, M. / Movileanu, L. / van den Berg, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.5 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3sy7C ![]() 3sy9C ![]() 3sysC ![]() 3szdC ![]() 3szvC ![]() 3t0sC ![]() 3t20C ![]() 3t24C 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 on special symmetry positions |
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Components
#1: Protein | Mass: 51457.297 Da / Num. of mol.: 1 / Fragment: unp residues 26-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 25% PEG 1000 0.2 M ammonium sulphate 50 mM Na-citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→50 Å / Num. obs: 18213 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.66→2.71 Å / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: P / Resolution: 2.7→9.993 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 27.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.632 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→9.993 Å
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Refine LS restraints |
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LS refinement shell |
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