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- PDB-5ks6: Recognition and targeting mechanisms by chaperones in flagella as... -

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Basic information

Entry
Database: PDB / ID: 5ks6
TitleRecognition and targeting mechanisms by chaperones in flagella assembly and operation
ComponentsFlagellar protein FliTFlagellum
KeywordsCHAPERONE / Flagella / chaperones / assembly factors
Function / homologyFlagellar protein FliT / Flagellar protein FliT / negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / protein folding / identical protein binding / cytosol / Flagellar protein FliT
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKhanra, N.K. / Rossi, P. / Economou, A. / Kalodimos, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094623 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Recognition and targeting mechanisms by chaperones in flagellum assembly and operation.
Authors: Khanra, N. / Rossi, P. / Economou, A. / Kalodimos, C.G.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Structure summary
Revision 1.3Sep 14, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.5Mar 23, 2022Group: Author supporting evidence / Data collection / Database references
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6Jun 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: Flagellar protein FliT


Theoretical massNumber of molelcules
Total (without water)13,7161
Polymers13,7161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7250 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Flagellar protein FliT / Flagellum


Mass: 13715.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliT, STM1962 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1N2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic23D HNCA
142isotropic23D 1H-15N NOESY
152isotropic23D 1H-13C NOESY aliphatic
182isotropic23D 1H-13C NOESY aromatic
171isotropic13D HNCO

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N; U-99% 2H] FliT, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2OU-[2H, 15N, 13C]triple labeled90% H2O/10% D2O
solution20.08 mM U-[2H,15N] 1H-13C-IVLMAT, 1H-13C-15N FY FliT, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 mM sodium azide, 90% H2O/10% D2O2H, 15N, IVLMAT 1H-13C methyls, FY 1H, 13C, 15N2H, 15N_methyl_aromatic90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMFliT[U-99% 13C; U-99% 15N; U-99% 2H]1
20 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
0.5 mMEDTAnatural abundance1
5 mMbeta-mercaptoethanolnatural abundance1
0.05 %sodium azidenatural abundance1
0.08 mMFliTU-[2H,15N] 1H-13C-IVLMAT, 1H-13C-15N FY2
20 mMpotassium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
0.5 mMEDTAnatural abundance2
5 mMbeta-mercaptoethanolnatural abundance2
0.05 mMsodium azidenatural abundance2
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.1Bruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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