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- PDB-2ofq: NMR Solution Structure of a complex between the VirB9/VirB7 inter... -

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Basic information

Entry
Database: PDB / ID: 2ofq
TitleNMR Solution Structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system
Components
  • TraN
  • TraO
KeywordsPROTEIN TRANSPORT/PROTEIN TRANSPORT / TraO / TraN / pKM101 / PROTEIN TRANSPORT-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


Immunoglobulin-like - #2500 / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesIncN plasmid R46 (others)
MethodSOLUTION NMR / simulated annealing
AuthorsHarris, R. / Bayliss, R. / Driscoll, P.C. / Waksman, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system
Authors: Bayliss, R. / Harris, R. / Coutte, L. / Monier, A. / Fronzes, R. / Christie, P.J. / Driscoll, P.C. / Waksman, G.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TraO
B: TraN


Theoretical massNumber of molelcules
Total (without water)13,3832
Polymers13,3832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TraO / Hypothetical protein


Mass: 10950.317 Da / Num. of mol.: 1 / Fragment: residues 177-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) IncN plasmid R46 (others) / Gene: traO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q79SE3
#2: Protein/peptide TraN


Mass: 2432.657 Da / Num. of mol.: 1 / Fragment: residues 21-42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) IncN plasmid R46 (others) / Gene: traN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q79SE5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 15N-separated NOESY
1443D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
115N VirB7, unlabelled virB9, 20mM sodium phosphate buffer, 0.1mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
215N,13C VirB7, unlabelled virB9, 20mM sodium phosphate buffer, 0.1mM EDTA, 100% D2O100% D2O
315N VirB9, unlabelled virB7, 20mM sodium phosphate buffer, 0.1mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
415N,13C VirB9, unlabelled virB7, 20mM sodium phosphate buffer, 0.1mM EDTA, 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger A. T. etall / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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