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- PDB-1q5f: NMR Structure of Type IVb pilin (PilS) from Salmonella typhi -

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Basic information

Entry
Database: PDB / ID: 1q5f
TitleNMR Structure of Type IVb pilin (PilS) from Salmonella typhi
ComponentsPilS
KeywordsCELL ADHESION / TYPE IVb PILIN / ALPHA-BETA ROLL / MONOMER
Function / homologyType 4 secretion system, PilS, N-terminal / PilS N terminal / TcpA-like pilin / TcpA-like pilin / membrane => GO:0016020 / 2-Layer Sandwich / Alpha Beta / PilS
Function and homology information
Biological speciesSalmonella typhi (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsXu, X.F. / Tan, Y.W. / Hackett, J. / Zhang, M. / Mok, Y.K.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: NMR Structure of a Type IVb Pilin from Salmonella typhi and Its Assembly into Pilus
Authors: Xu, X.F. / Tan, Y.W. / Lam, L. / Hackett, J. / Zhang, M. / Mok, Y.K.
History
DepositionAug 7, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PilS


Theoretical massNumber of molelcules
Total (without water)15,8421
Polymers15,8421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PilS / / Type IVb pilin


Mass: 15842.432 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: PilS / Plasmid: pET-H / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZIU9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1233D 15N-separated NOESY
133HNHA
144Amide proton exchange
NMR detailsText: The structures are based on a total of 2315 restraints, 2033 are NOE-derived distance constraints, 206 dihedral angle restraints, 76 distance restraints from hydrogen bonds.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM PilS U-15N, 13C; 50mM phosphate buffer; 0.5M sodium sulfate; 90% H2O, 10% D2O90% H2O/10% D2O
21mM PilS 10% 13C; 50mM phosphate buffer; 0.5M sodium sulfate; 90% H2O, 10% D2O90% H2O/10% D2O
31mM PilS U-15N; 50mM phosphate buffer; 0.5M sodium sulfate; 90% H2O, 10% D2O90% H2O/10% D2O
41mM PilS U-15N; 50mM phosphate buffer; 0.5M sodium sulfate; 90% H2O, 10% D2O100% D2O
Sample conditionsIonic strength: 0.55 / pH: 6.0 / Pressure: ambient / Temperature: 303 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
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRcollection
NMRPipeDelaglioprocessing
NMRViewJohnsondata analysis
DYANAGuentertstructure solution
CYANAGuentertstructure solution
Amber7Caserefinement
RefinementMethod: distance geometry, 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: 10

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