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- PDB-2rrl: Solution structure of the C-terminal domain of the FliK -

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Basic information

Entry
Database: PDB / ID: 2rrl
TitleSolution structure of the C-terminal domain of the FliK
ComponentsFlagellar hook-length control protein
KeywordsPROTEIN TRANSPORT / FliK / FlhB / bacterial flagella motor / hook-length control
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum assembly
Similarity search - Function
Transcription Regulator spoIIAA - #140 / Flagellar hook-length control protein FliK / FliK-like, C-terminal domain superfamily / Flagellar hook-length control protein-like, C-terminal / Flagellar hook-length control protein FliK / Transcription Regulator spoIIAA / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar hook-length control protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMizuno, S. / Tate, S. / Kobayashi, N. / Amida, H.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion apparatus
Authors: Mizuno, S. / Amida, H. / Kobayashi, N. / Aizawa, S. / Tate, S.
History
DepositionJan 2, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar hook-length control protein


Theoretical massNumber of molelcules
Total (without water)17,7741
Polymers17,7741
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Flagellar hook-length control protein / FliK


Mass: 17773.783 Da / Num. of mol.: 1 / Fragment: UNP residues 204-370
Source method: isolated from a genetically manipulated source
Details: substrate specificity switch (T3S4) domain / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P26416

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D HCACO
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D C(CO)NH
11113D HNCANNH
11213D HBHA(CO)NH
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11513D 1H-13C dec NOESY
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11822D 1H-13C HSQC aliphatic
11923D (H)CCH-TOCSY
12023D (H)CCH-COSY
12123D 1H-13C NOESY aliphatic
12232D 1H-15N HSQC
12333D 1H-15N NOESY
12433D 1H-15N TOCSY
12533D HNHA
12642D 1H-1H NOESY
12742D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-13C; U-15N] PROTEIN-1; 50mM sodium phosphate-2; 1mM EDTA-3; 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-13C; U-15N] PROTEIN-4; 50mM sodium phosphate-5; 1mM EDTA-6; 100% D2O100% D2O
31mM [U-15N] PROTEIN-7; 50mM sodium phosphate-8; 1mM EDTA-9; 90% H2O/10% D2O90% H2O/10% D2O
40.5mM [U-15N] PROTEIN-10; 50mM sodium phosphate-11; 1mM EDTA-12; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPROTEIN-1[U-13C; U-15N]1
50 mMsodium phosphate-21
1 mMEDTA-31
1 mMPROTEIN-4[U-13C; U-15N]2
50 mMsodium phosphate-52
1 mMEDTA-62
1 mMPROTEIN-7[U-15N]3
50 mMsodium phosphate-83
1 mMEDTA-93
0.5 mMPROTEIN-10[U-15N]4
50 mMsodium phosphate-114
1 mMEDTA-124
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TALOSCornilescu, Delaglio and Baxrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: 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: 15 / Representative conformer: 1

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