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- PDB-2wmz: Structure of a mutated TolC -

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Basic information

Entry
Database: PDB / ID: 2wmz
TitleStructure of a mutated TolC
ComponentsOUTER MEMBRANE PROTEIN TOLC
KeywordsMEMBRANE PROTEIN / TYPE-I SECRETION / CELL OUTER MEMBRANE / TRANSPORT / DRUG-EFFLUX
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity ...MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity / monoatomic ion transmembrane transport / cell outer membrane / response to organic cyclic compound / response to toxic substance / monoatomic ion channel activity / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding
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
TRIETHYLENE GLYCOL / Outer membrane protein TolC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHinchliffe, P. / Pei, X.Y. / Symmons, M.F. / Koronakis, E. / Hughes, C. / Koronakis, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / 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 3, 2009Deposition 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 1.3Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)141,68112
Polymers140,8013
Non-polymers8809
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16370 Å2
ΔGint-66.6 kcal/mol
Surface area56520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.690, 135.220, 136.470
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
22
33
44
55
66
77
88
99
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

NCS oper:
IDCodeMatrixVector
1given(-0.50531, -0.72483, -0.46828), (0.70181, -0.02944, -0.71175), (0.50212, -0.6883, 0.52357)-82.09022, -0.20813, 1.29388
2given(-0.49161, 0.71149, 0.5021), (-0.73022, -0.02268, -0.68283), (-0.47444, -0.70233, 0.53069)-40.76891, -58.58141, -39.16811

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Components

#1: Protein OUTER MEMBRANE PROTEIN TOLC / TOLC OUTER MEMBRANE PROTEIN


Mass: 46933.723 Da / Num. of mol.: 3
Fragment: MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PT7TOLC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL923(DE3) / Variant (production host): TOLC- / References: UniProt: P02930
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 389 TO SER ENGINEERED RESIDUE IN CHAIN B, ARG 389 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ARG 389 TO SER ENGINEERED RESIDUE IN CHAIN B, ARG 389 TO SER ENGINEERED RESIDUE IN CHAIN C, ARG 389 TO SER
Nonpolymer detailsTRIETHYLENE GLYCOL (PGE): FRAGMENT OF PRECIPITANT
Sequence detailsV TO L AT GENE POSITION 191 IN ISOLATE USED FOR STRUCTURE DETERMINATION - CORRESPONDS TO L169 IN ...V TO L AT GENE POSITION 191 IN ISOLATE USED FOR STRUCTURE DETERMINATION - CORRESPONDS TO L169 IN THE MATURE FORM OF PROTEIN CRYSTALLIZED

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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: 4.059 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 7
Details: 50 MM TRIS PH 8.2, 50 MM NACL, 14% PEG2000, 0.075% N-DODECYL-BETA-D-MALTOSIDE, 0.3% N-OCTYL BETA-D-GLUCOPYRANOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2009 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→29.93 Å / Num. obs: 51195 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 61.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→3.1 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.8 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK9 CHAIN A

1ek9


Resolution: 2.9→29.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2898038.02 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: GEOMETRIC REFINEMENT WAS CARRIED OUT USING CNS VERSION 1.1. B-FACTOR REFINEMENT, BULK SOLVENT MODELLING, AND FINAL R-FACTORS ARE FROM PHENIX. TRIETHYLENE GLYCOL PARAMETER FILE AND TOPOLOGY ...Details: GEOMETRIC REFINEMENT WAS CARRIED OUT USING CNS VERSION 1.1. B-FACTOR REFINEMENT, BULK SOLVENT MODELLING, AND FINAL R-FACTORS ARE FROM PHENIX. TRIETHYLENE GLYCOL PARAMETER FILE AND TOPOLOGY FILE WERE FROM HIC-UP DATABASE.
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2611 5.1 %RANDOM
Rwork0.258 ---
obs0.258 51195 98.9 %-
Solvent computationSolvent model: PHENIX FLAT BULK SOLVENT MODEL / Bsol: 24.73 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 59.6 Å2
Baniso -1Baniso -2Baniso -3
1-51.0078 Å20 Å20 Å2
2---22.77 Å20 Å2
3----28.2361 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a1.18 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9903 0 54 24 9981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINEDX-RAY DIFFRACTION0.04200
22X-RAY DIFFRACTION0.04200
33X-RAY DIFFRACTION0.07300
44X-RAY DIFFRACTION0.06100
55X-RAY DIFFRACTION0.06100
66X-RAY DIFFRACTION0.04200
77X-RAY DIFFRACTION0.06100
88X-RAY DIFFRACTION0.06100
99X-RAY DIFFRACTION0.06100
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.5 425 5.1 %
Rwork0.446 7909 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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