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- PDB-2vde: Crystal Structure of the Open State of TolC Outer Membrane Compon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vde | ||||||
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Title | Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps | ||||||
![]() | OUTER MEMBRANE PROTEIN TOLC | ||||||
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Function / homology | ![]() MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bavro, V.N. / Pietras, Z. / Furnham, N. / Perez-Cano, L. / Fernandez-Recio, J. / Pei, X.Y. / Truer, R. / Misra, R. / Luisi, B. | ||||||
![]() | ![]() Title: Assembly and Channel Opening in a Bacterial Drug Efflux Machine. Authors: Bavro, V.N. / Pietras, Z. / Furnham, N. / Perez-Cano, L. / Fernandez-Recio, J. / Pei, X.Y. / Truer, R. / Misra, R. / Luisi, B. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.3 KB | Display | ![]() |
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PDB format | ![]() | 202 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vddC ![]() 1ek9S 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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Unit cell |
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Components
#1: Protein | Mass: 50623.000 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-450 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, VAL 191 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 384 TO PHE ...ENGINEERED | Nonpolymer details | CHLORIDE ION (CL): CHLORIDE DEDUCED FROM COORDINATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.91 % / Description: NONE |
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Crystal grow![]() | pH: 10.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M CAPS PH10.5, 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 10, 2007 / Details: SLITS |
Radiation | Monochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→22.1 Å / Num. obs: 36034 / % possible obs: 97.7 % / Observed criterion σ(I): 2.4 / Redundancy: 5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.53 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.45 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1EK9 Resolution: 3.2→22.08 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.839 / Cross valid method: THROUGHOUT / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED IN FULL WITH OCCUPANCY ZERO.
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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: 67.82 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→22.08 Å
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Refine LS restraints |
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