+Open data
-Basic information
Entry | Database: PDB / ID: 6ene | ||||||
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Title | OmpF orthologue from Enterobacter cloacae (OmpE35) | ||||||
Components | Outer membrane protein (Porin) | ||||||
Keywords | TRANSPORT PROTEIN / Porine OmpF-orthologue / Outer Membrane | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | van den Berg, B. / Abellon-Ruiz, J. / Basle, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2018 Title: Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins. Authors: Acosta-Gutierrez, S. / Ferrara, L. / Pathania, M. / Masi, M. / Wang, J. / Bodrenko, I. / Zahn, M. / Winterhalter, M. / Stavenger, R.A. / Pages, J.M. / Naismith, J.H. / van den Berg, B. / ...Authors: Acosta-Gutierrez, S. / Ferrara, L. / Pathania, M. / Masi, M. / Wang, J. / Bodrenko, I. / Zahn, M. / Winterhalter, M. / Stavenger, R.A. / Pages, J.M. / Naismith, J.H. / van den Berg, B. / Page, M.G.P. / Ceccarelli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ene.cif.gz | 206.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ene.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ene.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/6ene ftp://data.pdbj.org/pub/pdb/validation_reports/en/6ene | HTTPS FTP |
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-Related structure data
Related structure data | 5o77C 5o79C 2zfgS 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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Unit cell |
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-Components
#1: Protein | Mass: 36291.305 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ompF, NCTC10005_05711 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M7H8A9 #2: Chemical | ChemComp-SO4 / #3: Sugar | ChemComp-BOG / | #4: Chemical | ChemComp-C8E / ( #5: 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: 3.64 Å3/Da / Density % sol: 66.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.05M Citric Acid 0.1M Lithium sulfate 0.05M Sodium phosphate dibasic 19% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.81 Å / Num. obs: 70576 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.99 / Rpim(I) all: 0.03 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4485 / CC1/2: 0.63 / Rpim(I) all: 0.56 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZFG Resolution: 2.3→45.835 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.835 Å
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Refine LS restraints |
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LS refinement shell |
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