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- PDB-2vdd: Crystal Structure of the Open State of TolC Outer Membrane Compon... -

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Basic information

Entry
Database: PDB / ID: 2vdd
TitleCrystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps
ComponentsOUTER MEMBRANE PROTEIN TOLC
KeywordsTRANSPORT PROTEIN / BETA BARREL / ALPHA HELICAL BARREL / MULTIDRUG EFFLUX PUMP / INTEGRAL MEMBRANE PROTEIN / OUTER MEMBRANE / MEMBRANE / TRANSPORT / TRANSMEMBRANE
Function / homology
Function and homology information


MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity ...MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity / monoatomic ion channel activity / cell outer membrane / response to organic cyclic compound / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane
Similarity search - Function
Type I secretion outer membrane protein, TolC / : / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux protein / Outer membrane efflux protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Outer membrane protein TolC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBavro, V.N. / Pietras, Z. / Furnham, N. / Perez-Cano, L. / Fernandez-Recio, J. / Pei, X.Y. / Truer, R. / Misra, R. / Luisi, B.
CitationJournal: Mol.Cell / Year: 2008
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
DepositionOct 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN TOLC
B: OUTER MEMBRANE PROTEIN TOLC
C: OUTER MEMBRANE PROTEIN TOLC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0939
Polymers151,8693
Non-polymers2246
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16390 Å2
ΔGint-83.6 kcal/mol
Surface area72790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)122.485, 70.966, 219.951
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein OUTER MEMBRANE PROTEIN TOLC


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.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET41B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C43, C41 / References: UniProt: P02930
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 191 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 384 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, VAL 191 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN A, ARG 389 TO GLU ENGINEERED RESIDUE IN CHAIN B, VAL 191 TO LEU ENGINEERED RESIDUE IN CHAIN B, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN B, ARG 389 TO GLU ENGINEERED RESIDUE IN CHAIN C, VAL 191 TO LEU ENGINEERED RESIDUE IN CHAIN C, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN C, ARG 389 TO GLU
Nonpolymer detailsCHLORIDE ION (CL): CHLORIDE ION DEDUCED FROM COORDINATION PATTERN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.18 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLISED FROM 0.1M HEPES 7.5, 5% ISOPROPANOL, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2007 / Details: SLITS
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.3→29.8 Å / Num. obs: 26721 / % possible obs: 98 % / Observed criterion σ(I): 2.4 / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.46
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.45 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK9 CHAIN A

1ek9


Resolution: 3.3→29.8 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.625 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.604 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REGIONS FOR WHICH NO ELECTRON DENSITY WAS OBSERVED WERE MODELLED IN FULL BUT WITH ZERO OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1425 5.1 %RANDOM
Rwork0.236 ---
obs0.239 26721 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.04 Å2
2---0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9908 0 6 1 9915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229983
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.95213563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09551278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60225.949506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.917151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6241556
X-RAY DIFFRACTIONr_chiral_restr0.0680.21577
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027667
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.24821
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.27093
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.2116
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3971.56374
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.727210211
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.56733666
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0264.53352
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.424 84
Rwork0.291 1787

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