+Open data
-Basic information
Entry | Database: PDB / ID: 3k19 | ||||||
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Title | OmpF porin | ||||||
Components | Outer membrane protein F | ||||||
Keywords | MEMBRANE PROTEIN / BETA BARREL / FOSCHOLINE-12 / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Cell membrane / Cell outer membrane / Ion transport / Membrane / Phage recognition / Porin / Transmembrane / Transport / TRANSPORT PROTEIN | ||||||
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 / protein transport ...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 / protein transport / monoatomic ion channel activity / lipid binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å | ||||||
Authors | Kefala, G. / Ahn, C. / Krupa, M. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. / Center for Structures of Membrane Proteins (CSMP) | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Structures of the OmpF porin crystallized in the presence of foscholine-12. Authors: Kefala, G. / Ahn, C. / Krupa, M. / Esquivies, L. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k19.cif.gz | 718.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k19.ent.gz | 600.2 KB | Display | PDB format |
PDBx/mmJSON format | 3k19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k19_validation.pdf.gz | 514.1 KB | Display | wwPDB validaton report |
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Full document | 3k19_full_validation.pdf.gz | 643.9 KB | Display | |
Data in XML | 3k19_validation.xml.gz | 144.2 KB | Display | |
Data in CIF | 3k19_validation.cif.gz | 190.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/3k19 ftp://data.pdbj.org/pub/pdb/validation_reports/k1/3k19 | HTTPS FTP |
-Related structure data
Related structure data | 3k1bC 2omfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 37114.250 Da / Num. of mol.: 12 / Fragment: sequence database residues 1-340 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: Bl21(DE3) / References: UniProt: P02931 |
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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: 4.35 Å3/Da / Density % sol: 71.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 0.4 M NaH2PO4/1.6 M K2HPO4, 0.2M sodium chloride, 0.1M Imidazole pH 8, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2008 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→100 Å / Num. obs: 74966 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 9.233 |
Reflection shell | Resolution: 3.8→3.87 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.667 / Rsym value: 0.488 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OMF Resolution: 3.79→49.57 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.749 / SU B: 35.787 / SU ML: 0.499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.741 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.133 Å2
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Refinement step | Cycle: LAST / Resolution: 3.79→49.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2619 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.01 Å
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LS refinement shell | Resolution: 3.787→3.885 Å / Total num. of bins used: 20
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