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- PDB-2xmn: High resolution snapshots of defined TolC open states present an ... -

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Basic information

Entry
Database: PDB / ID: 2xmn
TitleHigh resolution snapshots of defined TolC open states present an iris- like movement of periplasmic entrance helices
ComponentsOuter membrane protein TolC
KeywordsTRANSPORT PROTEIN / OUTER-MEMBRANE / DRUG-EFFLUX / TYPE-I SECRETION
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 / 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 / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / 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
Outer membrane protein TolC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPei, X.Y. / Koronakis, E. / Hughes, C. / Koronakis, V.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Structures of sequential open states in a symmetrical opening transition of the TolC exit duct.
Authors: Pei, X.Y. / Hinchliffe, P. / Symmons, M.F. / Koronakis, E. / Benz, R. / Hughes, C. / Koronakis, V.
History
DepositionJul 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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)141,3707
Polymers140,7533
Non-polymers6174
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-79.8 kcal/mol
Surface area61390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.124, 135.524, 136.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:171 OR RESSEQ 173:378 OR RESSEQ 380:399 OR RESSEQ 401: 428 )
211CHAIN B AND (RESSEQ 1:171 OR RESSEQ 173:378 OR RESSEQ 380:399 OR RESSEQ 401: 428 )
311CHAIN C AND (RESSEQ 1:171 OR RESSEQ 173:378 OR RESSEQ 380:399 OR RESSEQ 401: 428 )

NCS oper:
IDCodeMatrixVector
1given(-0.5069, 0.4783, 0.7172), (-0.4926, 0.522, -0.6963), (-0.7074, -0.7062, -0.02902)-46.23, 64.45, 94.93
2given(-0.496, -0.4972, -0.7119), (0.4817, 0.5246, -0.702), (0.7225, -0.6911, -0.02067)75.55, 55.12, 79.96

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Components

#1: Protein Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 46917.723 Da / Num. of mol.: 3 / Fragment: RESIDUES 23-450 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
Variant: C41 / Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN A, ARG 389 TO SER ...ENGINEERED RESIDUE IN CHAIN A, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN A, ARG 389 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN B, ARG 389 TO SER ENGINEERED RESIDUE IN CHAIN C, TYR 384 TO PHE ENGINEERED RESIDUE IN CHAIN C, ARG 389 TO SER
Sequence detailsV169L IS A KNOWN SEQUENCE (UNIPROT) DISCREPANCY.

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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: 4.4 Å3/Da / Density % sol: 72.06 % / Description: NONE
Crystal growpH: 7.4 / Details: PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2005 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→48 Å / Num. obs: 56719 / % possible obs: 89.7 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 51.94 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.1
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK9

1ek9


Resolution: 2.85→16.941 Å / SU ML: 0.42 / σ(F): 1.22 / Phase error: 39.33 / Stereochemistry target values: ML
Details: STATISTICAL DATA IN TABLE HEADED FIT TO DATA USED IN REFINEMENT (IN BINS), ARE PRESENTED FOR FULL ANOMALOUS DATA (BEFORE MERGING).
RfactorNum. reflection% reflection
Rfree0.3093 2630 5 %
Rwork0.2714 --
obs0.2733 56719 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.429 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 62.81 Å2
Baniso -1Baniso -2Baniso -3
1-61.9418 Å20 Å20 Å2
2---30.9723 Å20 Å2
3----30.9695 Å2
Refinement stepCycle: LAST / Resolution: 2.85→16.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9886 0 38 20 9944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110045
X-RAY DIFFRACTIONf_angle_d1.24413648
X-RAY DIFFRACTIONf_dihedral_angle_d19.4373691
X-RAY DIFFRACTIONf_chiral_restr0.0791596
X-RAY DIFFRACTIONf_plane_restr0.0041820
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3264X-RAY DIFFRACTIONPOSITIONAL
12B3264X-RAY DIFFRACTIONPOSITIONAL0.07
13C3273X-RAY DIFFRACTIONPOSITIONAL0.079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.88220.4781730.42442910X-RAY DIFFRACTION84
2.8822-2.9160.45681590.41773185X-RAY DIFFRACTION89
2.916-2.95140.46621740.42373406X-RAY DIFFRACTION96
2.9514-2.98850.41271610.41413517X-RAY DIFFRACTION99
2.9885-3.02760.42171990.40063468X-RAY DIFFRACTION98
3.0276-3.06890.44181930.37713462X-RAY DIFFRACTION99
3.0689-3.11240.42972190.38043468X-RAY DIFFRACTION99
3.1124-3.15860.45291600.35523513X-RAY DIFFRACTION98
3.1586-3.20760.34361810.35733456X-RAY DIFFRACTION99
3.2076-3.25990.42761800.35233555X-RAY DIFFRACTION99
3.2599-3.31570.40191810.34113447X-RAY DIFFRACTION99
3.3157-3.37550.40561920.32633511X-RAY DIFFRACTION99
3.3755-3.43990.35752020.31043502X-RAY DIFFRACTION99
3.4399-3.50950.36041840.28793503X-RAY DIFFRACTION99
3.5095-3.58510.34311900.29533448X-RAY DIFFRACTION99
3.5851-3.66770.3951850.33311909X-RAY DIFFRACTION95
3.7584-3.85890.29482120.26033387X-RAY DIFFRACTION99
3.8589-3.9710.29521820.26033539X-RAY DIFFRACTION99
3.971-4.09750.32041960.24523496X-RAY DIFFRACTION99
4.0975-4.24170.25651700.23643532X-RAY DIFFRACTION100
4.2417-4.40870.23822020.2183497X-RAY DIFFRACTION100
4.4087-4.60550.22181630.21043559X-RAY DIFFRACTION100
4.6055-4.84290.22212080.19813497X-RAY DIFFRACTION100
4.8429-5.13840.23742130.18963503X-RAY DIFFRACTION100
5.1384-5.52230.2481980.21413506X-RAY DIFFRACTION100
5.5223-6.05490.2911770.23863552X-RAY DIFFRACTION100
6.0549-6.87910.29991740.24263561X-RAY DIFFRACTION100
6.8791-8.48190.20171930.19893512X-RAY DIFFRACTION100
8.4819-16.94080.22941610.21023549X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32850.4638-0.16090.7567-0.69541.75060.0517-0.07280.12240.2654-0.10340.1638-0.60820.20550.04740.8549-0.13340.0320.49230.08220.527718.146336.636573.4784
20.33850.02850.23891.6251-1.52542.12110.0154-0.04080.02680.1914-0.00350.0868-0.1367-0.1413-0.02740.77930.03550.14380.5508-0.01650.5236-3.843431.280766.3433
30.27820.2062-0.11140.2676-0.35551.2153-0.0180.1098-0.0742-0.4179-0.1211-0.08960.45450.05270.15610.66320.11690.17530.49710.05530.523814.919123.402853.9371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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