+Open data
-Basic information
Entry | Database: PDB / ID: 5o78 | ||||||
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Title | Crystal structure of Omp35 from Enterobacter aerogenes | ||||||
Components | Phosphoporin PhoE | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane / trimer / porin / passive diffusion | ||||||
Function / homology | Function and homology information porin activity / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Enterobacter aerogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Ferrara, L. / Naismith, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Omp35 from Enterobacter aerogenes Authors: Ferrara, L. / Naismith, J. #1: Journal: To Be Published Title: Crystal structure of Omp35 from Enterobacter aerogenes Authors: Ferrara, L. / Naismith, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o78.cif.gz | 386 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o78.ent.gz | 323.1 KB | Display | PDB format |
PDBx/mmJSON format | 5o78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o78 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o78 | HTTPS FTP |
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-Related structure data
Related structure data | 1omf S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 7 - 337 / Label seq-ID: 7 - 337
NCS ensembles :
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-Components
#1: Protein | Mass: 37359.344 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ASV18_23685, BXQ27_19200 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A0F1QVM5, UniProt: A0A0H3FYJ7*PLUS #2: 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: 3.19 Å3/Da / Density % sol: 61.41 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium Chloride, 0.05 M magnesium sulfate, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→108.33 Å / Num. obs: 27313 / % possible obs: 85 % / Redundancy: 2.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.85→2.92 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1omf 1omf Resolution: 2.85→108.33 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.862 / SU B: 39.607 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.818 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→108.33 Å
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Refine LS restraints |
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