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- PDB-6ehf: OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ehf | ||||||
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Title | OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form) | ||||||
![]() | OmpT protein | ||||||
![]() | 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 / cell outer membrane / metal ion binding / OmpT protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den berg, B. / Pathania, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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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.) ![]() Gene: ompT, VC0395_A1445 / Plasmid: pET28 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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