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- PDB-4jml: Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) ... -

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Basic information

Entry
Database: PDB / ID: 4jml
TitleCrystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) complex.
Components
  • Colicin-E9
  • Protein TolB
KeywordsPROTEIN TRANSPORT/TOXIN / protein-protein interaction / engineered disulfide / bacteriocin transport / protein transport / PROTEIN TRANSPORT-TOXIN complex
Function / homology
Function and homology information


extrachromosomal circular DNA / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / protein domain specific binding / protein-containing complex / metal ion binding
Similarity search - Function
TolB, N-terminal domain / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / TolB, C-terminal domain ...TolB, N-terminal domain / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / TolB, C-terminal domain / His-Me finger superfamily / 6 Propeller / Neuraminidase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWojdyla, J.A. / Klein, A. / Kleanthous, C.
CitationJournal: Science / Year: 2013
Title: Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF.
Authors: Nicholas G Housden / Jonathan T S Hopper / Natalya Lukoyanova / David Rodriguez-Larrea / Justyna A Wojdyla / Alexander Klein / Renata Kaminska / Hagan Bayley / Helen R Saibil / Carol V ...Authors: Nicholas G Housden / Jonathan T S Hopper / Natalya Lukoyanova / David Rodriguez-Larrea / Justyna A Wojdyla / Alexander Klein / Renata Kaminska / Hagan Bayley / Helen R Saibil / Carol V Robinson / Colin Kleanthous /
Abstract: Porins are β-barrel outer-membrane proteins through which small solutes and metabolites diffuse that are also exploited during cell death. We have studied how the bacteriocin colicin E9 (ColE9) ...Porins are β-barrel outer-membrane proteins through which small solutes and metabolites diffuse that are also exploited during cell death. We have studied how the bacteriocin colicin E9 (ColE9) assembles a cytotoxic translocon at the surface of Escherichia coli that incorporates the trimeric porin OmpF. Formation of the translocon involved ColE9's unstructured N-terminal domain threading in opposite directions through two OmpF subunits, capturing its target TolB on the other side of the membrane in a fixed orientation that triggers colicin import. Thus, an intrinsically disordered protein can tunnel through the narrow pores of an oligomeric porin to deliver an epitope signal to the cell to initiate cell death.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TolB
E: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3963
Polymers46,3562
Non-polymers401
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-18 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.089, 81.420, 126.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein TolB


Mass: 44716.629 Da / Num. of mol.: 1 / Mutation: P201C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECDH1ME8569_0700, EcDH1_2895, tolB / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9R0N0
#2: Protein/peptide Colicin-E9


Mass: 1639.618 Da / Num. of mol.: 1 / Fragment: T-domain, Residues 32-47 / Mutation: A33C / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
References: UniProt: P09883, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80mM calcium chloride, 24% PEG 5000MME, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2013 / Details: mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→38.8 Å / % possible obs: 99 % / Observed criterion σ(I): 1.95 / Redundancy: 6.5 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 2→2.12 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.95 / Num. unique all: 8681 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
GDAClientdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ivz

2ivz


Resolution: 2→38.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.179 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1440 5 %RANDOM
Rwork0.1688 ---
obs0.1717 28548 99.47 %-
all-28700 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.66 Å2 / Biso mean: 34.4006 Å2 / Biso min: 16.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---1.78 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 1 282 3372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193240
X-RAY DIFFRACTIONr_bond_other_d0.0010.022981
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9394432
X-RAY DIFFRACTIONr_angle_other_deg0.8353.0016861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88524.702151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2481519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 89 -
Rwork0.242 1821 -
all-1910 -
obs--92.85 %

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