+Open data
-Basic information
Entry | Database: PDB / ID: 5fvn | |||||||||||||||
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Title | X-ray crystal structure of Enterobacter cloacae OmpE36 porin. | |||||||||||||||
Components | OMPC PORIN | |||||||||||||||
Keywords | MEMBRANE PROTEIN / PORIN / OUTER MEMBRANE PROTEIN / CHANNEL / LPS / TRIMER | |||||||||||||||
Function / homology | Function and homology information porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ENTEROBACTER CLOACAE (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||||||||
Authors | Arunmanee, W. / Pathania, M. / Soloyova, A. / Brun, A. / Ridley, H. / Basle, A. / van den Berg, B. / Lakey, J.H. | |||||||||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis. Authors: Arunmanee, W. / Pathania, M. / Solovyova, A.S. / Le Brun, A.P. / Ridley, H. / Basle, A. / van den Berg, B. / Lakey, J.H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fvn.cif.gz | 957.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fvn.ent.gz | 797.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fvn_validation.pdf.gz | 8 MB | Display | wwPDB validaton report |
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Full document | 5fvn_full_validation.pdf.gz | 7.9 MB | Display | |
Data in XML | 5fvn_validation.xml.gz | 100.1 KB | Display | |
Data in CIF | 5fvn_validation.cif.gz | 146 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/5fvn ftp://data.pdbj.org/pub/pdb/validation_reports/fv/5fvn | HTTPS FTP |
-Related structure data
Related structure data | 2j1nS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 37907.602 Da / Num. of mol.: 6 / Fragment: RESIDUES 22-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROBACTER CLOACAE (bacteria) / Plasmid: PBAD24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): OMP8 / References: UniProt: Q93K99 |
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-Sugars , 4 types, 12 molecules
#2: Polysaccharide | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | |
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-Non-polymers , 8 types, 2017 molecules
#5: Chemical | #6: Chemical | ChemComp-C8E / ( #7: Chemical | ChemComp-PO4 / #9: Chemical | ChemComp-FTT / #10: Chemical | ChemComp-MYR / #11: Chemical | ChemComp-DAO / #12: Chemical | #13: 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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.4M AMMONIUM SULFATE, 0.1M MES, 10% W/V PEG 3350, PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→48.92 Å / Num. obs: 529555 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J1N Resolution: 1.45→115.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.491 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.211 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→115.99 Å
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