+Open data
-Basic information
Entry | Database: PDB / ID: 4frx | ||||||
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Title | Crystal Structure of Pseudomonas aeruginosa OccK8 (OprE) | ||||||
Components | Anaerobically-induced outer membrane porin OprE | ||||||
Keywords | TRANSPORT PROTEIN / beta-barrel / transporter (porin) / outer membrane | ||||||
Function / homology | Function and homology information outer membrane / channel activity / porin activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Eren, E. / van den Berg, B. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of OccK Subfamily Proteins Authors: Eren, E. / 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 | 4frx.cif.gz | 326.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4frx.ent.gz | 266 KB | Display | PDB format |
PDBx/mmJSON format | 4frx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/4frx ftp://data.pdbj.org/pub/pdb/validation_reports/fr/4frx | HTTPS FTP |
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-Related structure data
Related structure data | 4frtC 4fsoC 4fspC 4ft6C 3sysS S: Starting model for refinement 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47579.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprE, PA0291 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XDA5 #2: Chemical | ChemComp-C8E / ( #3: 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: 3.39 Å3/Da / Density % sol: 63.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG 400, 0.2M ammonium sulphate, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012 |
Radiation | Monochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 99602 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rsym value: 0.118 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.93 / Num. unique all: 4913 / Rsym value: 0.553 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SYS Resolution: 1.9→14.993 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 22.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.336 Å2 / ksol: 0.44 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→14.993 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 31.2622 Å / Origin y: -6.8936 Å / Origin z: 74.2133 Å
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Refinement TLS group | Selection details: all |