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- PDB-5wip: TraE protein in complex with 2-(2-furyl)isonicotinic acid -

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Basic information

Entry
Database: PDB / ID: 5wip
TitleTraE protein in complex with 2-(2-furyl)isonicotinic acid
ComponentsConjugal transfer protein
KeywordsPROTEIN TRANSPORT / Type IV Secretion System / Fragment-Based Drug Design / Complex / Inhibitor / Antimicrobial Resistance / Bacterial secretion / VirB
Function / homology
Function and homology information


protein secretion by the type IV secretion system / membrane
Similarity search - Function
VirB8 protein / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
2-(furan-2-yl)pyridine-4-carboxylic acid / Conjugal transfer protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsCasu, B. / Arya, T. / Bessette, B. / Baron, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR MOP-84239 Canada
CitationJournal: Sci Rep / Year: 2017
Title: Fragment-based screening identifies novel targets for inhibitors of conjugative transfer of antimicrobial resistance by plasmid pKM101.
Authors: Casu, B. / Arya, T. / Bessette, B. / Baron, C.
History
DepositionJul 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conjugal transfer protein
B: Conjugal transfer protein
C: Conjugal transfer protein
D: Conjugal transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4625
Polymers75,2724
Non-polymers1891
Water2,630146
1
A: Conjugal transfer protein
D: Conjugal transfer protein
hetero molecules


  • defined by author
  • Evidence: assay for oligomerization, Bacterial two-hybrid assay corroborates the dimer form, cross-linking, Crosslinking experiments with DSS show formation of homomultimeric forms, gel filtration, ...Evidence: assay for oligomerization, Bacterial two-hybrid assay corroborates the dimer form, cross-linking, Crosslinking experiments with DSS show formation of homomultimeric forms, gel filtration, Analytic gel filtration corroborates the dimeric form
  • 37.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)37,8253
Polymers37,6362
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conjugal transfer protein
C: Conjugal transfer protein


Theoretical massNumber of molelcules
Total (without water)37,6362
Polymers37,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.390, 124.089, 109.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Conjugal transfer protein / Conjugal transfer protein TraE / TraE / TraE protein / Inner membrane protein forms channel for ...Conjugal transfer protein TraE / TraE / TraE protein / Inner membrane protein forms channel for type IV secretion of T-DNA complex / VirB8 / Type IV secretion of T-DNA VirB8 / Type IV secretion system protein VirB8


Mass: 18818.104 Da / Num. of mol.: 4 / Fragment: residues 70-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: traE, B634_00049, BE957_00530, ECONIH1_27615, pec386IL_00125, pEcNDM0_00049, pHKU1_33, pKC394-028, pKC396-021, pMUR050_041, pN3_023
Plasmid: PHT / Cell line (production host): BL21(DE3)STAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q17U16
#2: Chemical ChemComp-XXO / 2-(furan-2-yl)pyridine-4-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16% (w/v) PEG 10,000, 50 mM Bis-Tris (pH 5.5), 100 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.619→41.651 Å / Num. obs: 23012 / % possible obs: 98.1 % / Redundancy: 6 % / Rsym value: 0.172 / Net I/σ(I): 5.91

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.11.1_2575)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I97

5i97


Resolution: 2.62→41.65 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.11
RfactorNum. reflection% reflection
Rfree0.274 1546 6.72 %
Rwork0.217 --
obs0.221 23012 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.62→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 14 146 4644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014610
X-RAY DIFFRACTIONf_angle_d0.3896260
X-RAY DIFFRACTIONf_dihedral_angle_d9.9852740
X-RAY DIFFRACTIONf_chiral_restr0.041681
X-RAY DIFFRACTIONf_plane_restr0.002810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.619-2.70350.33111360.24971854X-RAY DIFFRACTION94
2.7035-2.80010.3421280.26021860X-RAY DIFFRACTION95
2.8001-2.91220.34051350.25891881X-RAY DIFFRACTION96
2.9122-3.04470.33431380.25291925X-RAY DIFFRACTION98
3.0447-3.20520.30021420.261949X-RAY DIFFRACTION98
3.2052-3.40590.34961410.23861935X-RAY DIFFRACTION99
3.4059-3.66870.27611430.21681990X-RAY DIFFRACTION99
3.6687-4.03770.30541430.21281972X-RAY DIFFRACTION100
4.0377-4.62130.23861450.17692007X-RAY DIFFRACTION100
4.6213-5.81980.22851460.18482005X-RAY DIFFRACTION100
5.8198-41.6560.22371490.22072088X-RAY DIFFRACTION99

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