[English] 日本語
Yorodumi- PDB-3pou: Crystal structure of E.coli OmpF porin in lipidic cubic phase: sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pou | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, large 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: 2.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pou.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pou.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3pou ftp://data.pdbj.org/pub/pdb/validation_reports/po/3pou | HTTPS FTP |
---|
-Related structure data
Related structure data | 3poqC 3poxC 2omfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 | ||
---|---|---|---|
#2: Chemical | ChemComp-OLC / ( #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.21 % / Mosaicity: 0.73 ° |
---|---|
Crystal grow | Temperature: 296 K / pH: 5.6 Details: 0.1M sodium citrate, 0.7M sodium tartrate, 1.0M potassium thiocyanate, pH 5.6, lipidic sponge phase, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2008 / 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: 2.8→19.99 Å / Num. all: 12017 / Num. obs: 12017 / % possible obs: 99.7 % / Redundancy: 9 % / Biso Wilson estimate: 52.1 Å2 / Rsym value: 0.329 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.014 / Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OMF Resolution: 2.8→19.99 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2364 / WRfactor Rwork: 0.1815 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8383 / SU B: 13.28 / SU ML: 0.264 / SU R Cruickshank DPI: 2.1879 / SU Rfree: 0.3554 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.03 Å2 / Biso mean: 48.0181 Å2 / Biso min: 24.7 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
|