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Yorodumi- PDB-6ehf: OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ehf | ||||||
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Title | OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form) | ||||||
Components | OmpT protein | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane protein / Porin / OmpF or OmpC ortholog / ion-transport / membrane beta barrel / ion-channel / diffusion porin / diffusion channel / non-specific porin. | ||||||
Function / homology | Gram-negative porin / Porin domain, Gram-negative type / Porin domain superfamily / porin activity / pore complex / monoatomic ion transport / cell outer membrane / OmpT protein Function and homology information | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | van den berg, B. / Pathania, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2018 Title: Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae. Authors: Pathania, M. / Acosta-Gutierrez, S. / Bhamidimarri, S.P. / Basle, A. / Winterhalter, M. / Ceccarelli, M. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ehf.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ehf.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ehf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/6ehf ftp://data.pdbj.org/pub/pdb/validation_reports/eh/6ehf | HTTPS FTP |
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-Related structure data
Related structure data | 5oykC 6ehbC 6ehcC 6ehdSC 6eheC 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: 34781.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: KEGG entry VC0395_A1445 Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria) Gene: ompT, VC0395_A1445 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AME7 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.05 M calcium chloride dihydrate, 0.05 M barium chloride, 0.1 M tris, 32% PEG 400 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→71.03 Å / Num. obs: 18714 / % possible obs: 99 % / Redundancy: 42.2 % / CC1/2: 1 / Rpim(I) all: 0.025 / Net I/σ(I): 22.1 |
Reflection shell | Highest resolution: 2.72 Å / Redundancy: 43.7 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.6 / Rpim(I) all: 0.679 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EHD Resolution: 2.72→71.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.094 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.29 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.065 Å2
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Refinement step | Cycle: 1 / Resolution: 2.72→71.03 Å
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Refine LS restraints |
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