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Open data
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Basic information
Entry | Database: PDB / ID: 3sy7 | ||||||
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Title | Improved crystal structure of Pseudomonas aeruginosa OprD | ||||||
![]() | Porin D | ||||||
![]() | MEMBRANE PROTEIN / beta-barrel / channel / outer membrane | ||||||
Function / homology | ![]() basic amino acid transport / oligosaccharide transport / outer membrane / porin activity / pore complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / monoatomic ion transport / serine-type peptidase activity / cell outer membrane / proteolysis 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 | ![]() | 166.1 KB | Display | ![]() |
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PDB format | ![]() | 131.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sy9C ![]() 3sybC ![]() 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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Details | Probable. |
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Components
#1: Protein | Mass: 46950.195 Da / Num. of mol.: 1 / Fragment: unp residues 24-443 / Mutation: V140F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32722, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||||
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#2: Chemical | ChemComp-C8E / ( #3: Water | ChemComp-HOH / | Sequence details | AUTHORS HAVE STATED THAT THE RESIDUE 140 IS INDEED A VAL AND NOT A PHE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 5.5 Details: 2 M ammonium sulphate 50 mM Na-citrate, pH 5.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 34239 / Num. obs: 33554 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.7 |
Reflection shell | Resolution: 2.15→2.19 Å / % possible all: 80.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.542 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→19.993 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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