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

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Basic information

Entry
Database: PDB / ID: 5krw
TitleRecognition and targeting mechanisms by chaperones in flagella assembly and operation
ComponentsFlagellar protein FliT,Flagellar hook-associated protein 2 fusionFlagellum
KeywordsCHAPERONE / Flagella / chaperones / assembly factors
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum organization / bacterial-type flagellum-dependent cell motility / protein folding / cell adhesion / extracellular region / identical protein binding / cytosol
Similarity search - Function
Flagellar protein FliT / Flagellar protein FliT / Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif
Similarity search - Domain/homology
Flagellar protein FliT / Flagellar hook-associated protein 2
Similarity search - Component
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 14, 2016Group: Database references
Revision 1.3Sep 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 1.4Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar protein FliT,Flagellar hook-associated protein 2 fusion


Theoretical massNumber of molelcules
Total (without water)17,3881
Polymers17,3881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9160 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,Flagellar hook-associated protein 2 fusion / Flagellum / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 17387.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria), (gene. exp.) Salmonella typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliT, STM1962, fliD, flaV, flbC, STM1960 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1N2, UniProt: P16328

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HN(CA)CB
133isotropic23D 1H-15N NOESY
144isotropic22D 1H-13C HSQC aromatic
154isotropic12D 1H-13C HSQC
1104isotropic13D (H)CCH-TOCSY
193isotropic22D 1H-15N HSQC
183isotropic23D 1H-13C NOESY
174isotropic23D 1H-13C NOESY aromatic
161isotropic13D HNCA

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N; U-99% 2H] FliT-FliD_fusion, 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
solution31 mM U[15N,2H] 1H-13C-ILVMAT-methyl FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O15N,2H, ILVMAT 1H-13C methyls15N methyl90% H2O/10% D2O
solution41 mM [U-99% 13C; U-99% 15N] FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2OU-13C-15Ndouble labeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMFliT-FliD_fusion[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
1 mMFliT-FliD_fusionU[15N,2H] 1H-13C-ILVMAT-methyl3
20 mMpotassium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
0.5 mMEDTAnatural abundance3
5 mMbeta-mercaptoethanolnatural abundance3
0.05 %sodium azidenatural abundance3
1 mMFliT-FliD_fusion[U-99% 13C; U-99% 15N]4
20 mMpotassium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
0.5 mMEDTAnatural abundance4
5 mMbeta-mercaptoethanolnatural abundance4
0.05 %sodium azidenatural abundance4
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8502

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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
TopSpin3.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
NMRViewJohnson, One Moon Scientificdata analysis
PSVSBhattacharya and Montelionedata analysis
PdbStat1.5tejero and montelionedata analysis
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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