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- PDB-1ek9: 2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1ek9
Title2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN AND EFFLUX PUMP COMPONENT FROM ESCHERICHIA COLI
ComponentsOUTER MEMBRANE PROTEIN TOLC
KeywordsMEMBRANE PROTEIN / Integral membrane protein / Alpha helical Barrel / Beta Barrel
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / porin activity / bile acid and bile salt transport ...MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / porin activity / bile acid and bile salt transport / monoatomic ion channel activity / efflux transmembrane transporter activity / cell outer membrane / 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
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Type I secretion outer membrane protein, TolC / : / 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 / Resolution: 2.1 Å
AuthorsKoronakis, V. / Sharff, A.J. / Koronakis, E. / Luisi, B. / Hughes, C.
Citation
Journal: Nature / Year: 2000
Title: Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export.
Authors: Koronakis, V. / Sharff, A. / Koronakis, E. / Luisi, B. / Hughes, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Oxidation of Selenomethionine: Some MADness in the Method!
Authors: Sharff, A.J. / Koronakis, E. / Luisi, B. / Koronakis, V.
History
DepositionMar 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,7153
Polymers141,7153
Non-polymers00
Water27,1671508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-50 kcal/mol
Surface area57500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.049, 265.049, 95.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a homo-trimer constructed from chains A, B and C

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Components

#1: Protein OUTER MEMBRANE PROTEIN TOLC


Mass: 47238.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PACYC184 / Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1508 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, ...Details: PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.6 %detergent mixture1drop
21.5 %1,2,3-heptanetriol1drop
37 %mPEG20001drop
410 %PEG4001drop
510 mM1dropNaCl
620 mMTris-HCl1drop
710-15 mg/mlprotein1drop
812.5 %mPEG20001reservoir
9400 mM1reservoirNaCl
1020 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→129 Å / Num. all: 146143 / Num. obs: 1388136 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.261 / Num. unique all: 15808 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 146143 / Num. measured all: 1388136
Reflection shell
*PLUS
% possible obs: 99.6 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
SHARPphasing
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The coordinates deposited are of the selenomethione substituted protein. Methionine residues at positions 4, 78, 279, 297 and 358 have been replaced with selenomethionine.
RfactorNum. reflectionSelection details
Rfree0.257 5841 Random - by resolution shell
Rwork0.208 --
all0.208 146020 -
obs0.208 146020 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9918 0 0 1508 11426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg1.3
Software
*PLUS
Name: 'BUSTER/TNT' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.88 Å2

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