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- PDB-1tqq: Structure of TolC in complex with hexamminecobalt -

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Basic information

Entry
Database: PDB / ID: 1tqq
TitleStructure of TolC in complex with hexamminecobalt
ComponentsOuter membrane protein tolC
KeywordsTRANSPORT PROTEIN / Beta-barrel / alpha-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 / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / porin activity ...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 / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / porin activity / 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
COBALT HEXAMMINE(III) / Outer membrane protein TolC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHiggins, M.K. / Eswaran, J. / Edwards, P.C. / Schertler, G.F. / Hughes, C. / Koronakis, V.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug effllux protein TolC
Authors: Higgins, M.K. / Eswaran, J. / Edwards, P.C. / Schertler, G.F. / Hughes, C. / Koronakis, V.
History
DepositionJun 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6904
Polymers154,5293
Non-polymers1611
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-42 kcal/mol
Surface area58800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.276, 265.276, 96.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 3 / Auth seq-ID: 1 - 428 / Label seq-ID: 1 - 428

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Outer membrane protein tolC


Mass: 51509.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TOLC, MTCB, MUKA, REFI, B3035 / Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 4.69 Å3/Da / Density % sol: 73.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% ...Details: 0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% polyethylene glycol 2000 monomethyl ether, 10% polyethylene glycol 400, 10mM NaCl, 20mM MgCl2, 20mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2002
RadiationMonochromator: Liquid gallium cooled, bent, triangular, si 111 optimised for: 1.2 (top crystal, 9.3 asymmetric cut) 1.488 (bottom crystal, 11.7 asymmetric cut)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 65599 / Num. obs: 62730 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rsym value: 0.095 / Net I/σ(I): 5.1
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.1 / Num. unique all: 63790 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1EK9

1ek9


Resolution: 2.75→30.43 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.841 / SU B: 10.299 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / ESU R: 0.555 / ESU R Free: 0.359
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.30473 3174 5.1 %RANDOM
Rwork0.26376 ---
all0.26579 65599 --
obs0.2657 59556 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.736 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9915 0 7 305 10227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02110047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.94913653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60951281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.21587
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027698
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.24610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5370.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5330.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5981.56390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.339210245
X-RAY DIFFRACTIONr_scbond_it2.44933657
X-RAY DIFFRACTIONr_scangle_it4.054.53408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1712tight positional0.070.05
2B1712tight positional0.070.05
3C1712tight positional0.070.05
1A1594loose positional0.385
2B1594loose positional0.375
3C1594loose positional0.395
1A1712tight thermal0.150.5
2B1712tight thermal0.150.5
3C1712tight thermal0.150.5
1A1594loose thermal2.610
2B1594loose thermal2.3110
3C1594loose thermal2.5610
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 255
Rwork0.347 4324

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