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- PDB-5kp0: Recognition and targeting mechanisms by chaperones in flagella as... -

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Basic information

Entry
Database: PDB / ID: 5kp0
TitleRecognition and targeting mechanisms by chaperones in flagella assembly and operation
ComponentsFlagellar protein FliT,Flagellum-specific ATP synthaseFlagellum
KeywordsCHAPERONE / flagella / chaperones / assembly factors
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / type III protein secretion system complex / protein secretion by the type III secretion system / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / type III protein secretion system complex / protein secretion by the type III secretion system / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / protein folding / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Flagellar export ATPase FliI, clade 1 / Flagellar protein FliT / Flagellar protein FliT / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain ...Flagellar export ATPase FliI, clade 1 / Flagellar protein FliT / Flagellar protein FliT / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Flagellar protein FliT / Flagellum-specific ATP synthase
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 1, 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 1.3Mar 23, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _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,Flagellum-specific ATP synthase


Theoretical massNumber of molelcules
Total (without water)15,6561
Polymers15,6561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8390 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-specific ATP synthase / Flagellum


Mass: 15656.003 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, fliI, fla AIII, flaC, STM1972 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A1N2, UniProt: P26465, H+-transporting two-sector ATPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
132isotropic23D HN(CA)CB
141isotropic23D 1H-15N NOESY
151isotropic23D 1H-13C NOESY
162isotropic23D HNCO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W protein, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 0.5 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O2H,15N_methyl_aromatic90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N; U-99% 2H] protein, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 0.5 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2Otriple labeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein[U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W1
20 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
5 mMbeta-mercaptoethanolnatural abundance1
0.5 mMEDTAnatural abundance1
0.05 %sodium azidenatural abundance1
0.5 mMprotein[U-99% 13C; U-99% 15N; U-99% 2H]2
20 mMpotassium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
5 mMbeta-mercaptoethanolnatural abundance2
0.5 mMEDTAnatural abundance2
0.05 %sodium azidenatural abundance2
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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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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