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- PDB-7qyi: Solution structure of the DNA-binding minor pilin FimT from Legio... -

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Basic information

Entry
Database: PDB / ID: 7qyi
TitleSolution structure of the DNA-binding minor pilin FimT from Legionella pneumophila
ComponentsPilus assembly protein
KeywordsDNA BINDING PROTEIN / type IV pilin
Function / homologyGeneral secretion pathway, GspH / Type II transport protein GspH / Prokaryotic N-terminal methylation site. / protein secretion by the type II secretion system / Prokaryotic N-terminal methylation site / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane / Pilus assembly protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsBraus, S.A.G. / Hospenthal, M.K. / Gossert, A.D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPR00P3_179728 Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: The molecular basis of FimT-mediated DNA uptake during bacterial natural transformation.
Authors: Braus, S.A.G. / Short, F.L. / Holz, S. / Stedman, M.J.M. / Gossert, A.D. / Hospenthal, M.K.
History
DepositionJan 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)14,3791
Polymers14,3791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Pilus assembly protein


Mass: 14379.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_06370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S6F8Q3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D NOESY combined
121isotropic23D (H)CCH-TOCSY
131isotropic33D HN(CA)CB
141isotropic33D CBCA(CO)NH
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 580 uM [U-13C; U-15N] FimT, 25 mM NaPi, 150 mM sodium chloride, 90% H2O/10% D2O
Label: u-15N,13C FimT / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
580 uMFimT[U-13C; U-15N]1
25 mMNaPinatural abundance1
150 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 150 mM NaCl mM / Label: Conditions_1 / pH: 7.2 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9001
Bruker AVANCE III HDBrukerAVANCE III HD6002
Bruker AVANCE NEOBrukerAVANCE NEO7003

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CcpNmr Analysis2.51CCPNpeak picking
CYANA3.98.2Guntert, Mumenthaler and Wuthrichstructure calculation
Amber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
TopSpin4.07Bruker Biospincollection
Refinement
MethodSoftware ordinal
simulated annealing3
molecular dynamics4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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