+Open data
-Basic information
Entry | Database: PDB / ID: 3t0s | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa OccK4 (OpdL) | ||||||
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: 2.2 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 | 3t0s.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t0s.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 3t0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t0s_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 3t0s_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 3t0s_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3t0s_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/3t0s ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t0s | HTTPS FTP |
-Related structure data
Related structure data | 3sy7C 3sy9C 3sybC 3sysC 3szdC 3szvC 3t20C 3t24C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44571.625 Da / Num. of mol.: 1 / Fragment: unp residues 28-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4137 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWP4 | ||
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#2: Chemical | ChemComp-C8E / ( #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% PEG400 50 mM NaCl 0.1 M Na-citrate, 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: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 29467 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.693 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 23.25 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.506 Å2 / ksol: 0.409 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.693 Å
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Refine LS restraints |
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LS refinement shell |
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