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Yorodumi- PDB-3poq: Crystal structure of E.coli OmpF porin in lipidic cubic phase: sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3poq | ||||||
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Title | Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small unit cell | ||||||
Components | OmpF protein | ||||||
Keywords | MEMBRANE PROTEIN / beta barrel / solute transport / pore | ||||||
Function / homology | Function and homology information colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity / lipid binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Efremov, R.G. / Sazanov, L.A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Structure of Escherichia coli OmpF porin from lipidic mesophase. Authors: Efremov, R.G. / Sazanov, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3poq.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3poq.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 3poq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3poq ftp://data.pdbj.org/pub/pdb/validation_reports/po/3poq | HTTPS FTP |
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-Related structure data
Related structure data | 3pouC 3poxC 2omfS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37114.250 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-362 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21List of strains of Escherichia coli / References: UniProt: C5W2U9, UniProt: P02931*PLUS | ||||
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#2: Chemical | ChemComp-OLC / ( #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 51.95 % / Description: THE FILE CONTAINS FRIEDEL PAIRS. / Mosaicity: 0.65 ° |
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Crystal grow | Temperature: 296 K / pH: 4.6 Details: 0.1M sodium acetate, 2.7M lithium nitrate, 2.0M potassium thiocyanate, pH 4.6, lipidic sponge phase, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Date: Nov 24, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2 cooled fixed exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→19.352 Å / Num. all: 27555 / Num. obs: 27555 / % possible obs: 91.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.22 Å2 / Rmerge(I) obs: 0.172 / Rsym value: 0.155 / Net I/σ(I): 6.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OMF Resolution: 1.9→19.352 Å / WRfactor Rwork: 0.2792 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: ML / Details: THE FILE CONTAINS FRIEDEL PAIRS.
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.794 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.43 Å2 / Biso min: 8.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.352 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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