+Open data
-Basic information
Entry | Database: PDB / ID: 3szd | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa OccK2 (OpdF) | ||||||
Components | porin | ||||||
Keywords | MEMBRANE PROTEIN / beta-barrel / channel / bacterial outer membrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.311 Å | ||||||
Authors | van den Berg, B. / Eren, E. | ||||||
Citation | Journal: Plos Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3szd.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3szd.ent.gz | 127.6 KB | Display | PDB format |
PDBx/mmJSON format | 3szd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3szd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3szd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3szd_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 3szd_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3szd ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3szd | HTTPS FTP |
-Related structure data
Related structure data | 3sy7C 3sy9C 3sybC 3sysC 3szvC 3t0sC 3t20C 3t24C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44710.430 Da / Num. of mol.: 2 / Fragment: unp residues 25-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6P8 #2: Chemical | ChemComp-C8E / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-3PE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 1K 50 mM Li2SO4 50 mM Na2SO4 50 mM Na-acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 27, 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: 2.31→50 Å / Num. obs: 37591 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.31→2.35 Å / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.311→14.995 Å / SU ML: 0.79 / σ(F): 1.41 / Phase error: 28.76 / 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: 39.07 Å2 / ksol: 0.406 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.311→14.995 Å
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Refine LS restraints |
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LS refinement shell |
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