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- PDB-5wio: TraE protein in complex with 4-(1H-pyrrol-1-yl)pyridine-2-carboxy... -

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Basic information

Entry
Database: PDB / ID: 5wio
TitleTraE protein in complex with 4-(1H-pyrrol-1-yl)pyridine-2-carboxylic 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
4-(1H-pyrrol-1-yl)pyridine-2-carboxylic acid / Conjugal transfer protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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

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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)75,4615
Polymers75,2724
Non-polymers1881
Water18010
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 shows homomultimer formation, gel filtration, Analytical ...Evidence: assay for oligomerization, Bacterial-two hybrid assay corroborates the dimer form, cross-linking, Crosslinking experiments with DSS shows homomultimer formation, gel filtration, Analytical gel filtration corroborates the dimerization
  • 37.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)37,8243
Polymers37,6362
Non-polymers1881
Water181
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.911, 125.535, 110.453
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-XXE / 4-(1H-pyrrol-1-yl)pyridine-2-carboxylic acid


Mass: 188.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
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: 2.52→39.478 Å / Num. obs: 26767 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rsym value: 0.151 / Net I/σ(I): 5.36

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I97

5i97


Resolution: 2.52→39.48 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.14
RfactorNum. reflection% reflection
Rfree0.356 1622 6.06 %
Rwork0.3 --
obs0.3 26767 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4441 0 14 10 4465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024716
X-RAY DIFFRACTIONf_angle_d0.5016395
X-RAY DIFFRACTIONf_dihedral_angle_d11.1111755
X-RAY DIFFRACTIONf_chiral_restr0.021688
X-RAY DIFFRACTIONf_plane_restr0.003829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5201-2.59420.42521330.37212058X-RAY DIFFRACTION100
2.5942-2.67790.39781340.3572078X-RAY DIFFRACTION100
2.6779-2.77360.39791330.34732050X-RAY DIFFRACTION100
2.7736-2.88460.42611340.35822086X-RAY DIFFRACTION100
2.8846-3.01590.43351340.35192082X-RAY DIFFRACTION100
3.0159-3.17480.43561330.35572064X-RAY DIFFRACTION100
3.1748-3.37360.40191350.34192097X-RAY DIFFRACTION100
3.3736-3.63390.38591350.32022090X-RAY DIFFRACTION100
3.6339-3.99930.3581360.32862103X-RAY DIFFRACTION100
3.9993-4.57730.37171350.2662097X-RAY DIFFRACTION100
4.5773-5.7640.32321390.2682144X-RAY DIFFRACTION100
5.764-39.48320.27561410.24992196X-RAY DIFFRACTION99

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