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- PDB-1djm: SOLUTION STRUCTURE OF BEF3-ACTIVATED CHEY FROM ESCHERICHIA COLI -

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Entry
Database: PDB / ID: 1djm
TitleSOLUTION STRUCTURE OF BEF3-ACTIVATED CHEY FROM ESCHERICHIA COLI
ComponentsCHEMOTAXIS PROTEIN Y
KeywordsSIGNALING PROTEIN / BEFX / CHEY / RESPONSE REGULATOR / CHEMOTAXIS / TWO-COMPONENT
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / internal peptidyl-lysine acetylation / regulation of chemotaxis / thermotaxis / bacterial-type flagellum / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / internal peptidyl-lysine acetylation / regulation of chemotaxis / thermotaxis / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / cytoplasm
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCho, H.S. / Lee, S.Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G.
Citation
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Beryllofluoride Mimics Phosphorylation of NtrC and Other Bacterial Response Regulators
Authors: Yan, D. / Cho, H.S. / Hastings, C.A. / Igo, M.M. / Lee, S.Y. / Pelton, J.G. / Stewart, V. / Wemmer, D.E. / Kustu, S.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 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: CHEMOTAXIS PROTEIN Y


Theoretical massNumber of molelcules
Total (without water)14,1121
Polymers14,1121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)27 / 60structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein CHEMOTAXIS PROTEIN Y


Mass: 14112.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-SEPARATED NOESY
1214D 13C/15N-SEPARATED NOESY
2323D 15N-SEPARATED NOESY
24215N HMQC-J
15113C CONSTANT-TIME HMQC-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
14 MM CHEY U-15N, 13C, 16 MM BECL2, 100 MM NAF, 20 MM MGCL2, PH 6.7
23 MM U-15N, 16 MM BECL2, 100 MM NAF, 20 MM MGCL2, PH 6.7
33 MM U-10% 13C, 16 MM BECL2, 100 MM NAF, 20 MM MGCL2, PH 6.7
42 MM CHEY, 16 MM BECL2, 100 MM NAF, 20 MM MGCL2, PH 6.7
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
116 mM BECL2, 100 mM NAF, 20 mM MGCL2 6.7AMBIENT 298 K
216 mM BECL2, 100 mM NAF, 20 mM MGCL2 6.7AMBIENT 298 K
316 mM BECL2, 100 mM NAF, 20 mM MGCL2 6.7AMBIENT 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUNTERT, MUMENTHALER, WUTHRICHstructure solution
OPAL2.2LUGINBUHL, GUNTERT, BILLETER, WUTHRICHrefinement
NMRPipe1.7DELAGLIO, BRZESIEK, VUISTER, ZHU, PFEIFER, BAXprocessing
XEASY1.3.11BARTELS, XIA, BILLETER, GUNTERT, WUTHRICHprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 972 NON-TRIVIAL NOE RESTRAINTS (213 INTRA RESIDUE, 271 SEQUENTIAL, 238 MEDIUM-RANGE, AND 250 LONG-RANGE). 78 PHI TORSION ANGLE RESTRAINTS AND 17 CHI1 ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 972 NON-TRIVIAL NOE RESTRAINTS (213 INTRA RESIDUE, 271 SEQUENTIAL, 238 MEDIUM-RANGE, AND 250 LONG-RANGE). 78 PHI TORSION ANGLE RESTRAINTS AND 17 CHI1 RESTRAINTS WERE USED. 47 HYDROGEN BONDS ( 94 UPPER AND LOWER DISTANCE RESTRAINTS) WERE USED IN LATER STAGES OF REFINEMENT.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 27

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