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- PDB-1dc7: STRUCTURE OF A TRANSIENTLY PHOSPHORYLATED "SWITCH" IN BACTERIAL S... -

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Basic information

Entry
Database: PDB / ID: 1dc7
TitleSTRUCTURE OF A TRANSIENTLY PHOSPHORYLATED "SWITCH" IN BACTERIAL SIGNAL TRANSDUCTION
ComponentsNITROGEN REGULATION PROTEIN
KeywordsSIGNALING PROTEIN / RECEIVER DOMAIN / PHOSPHORYLATION / SIGNAL TRANSDUCTION / CONFORMATIONAL REARRANGEMENT / TWO-COMPONENT SYSTEM
Function / homology
Function and homology information


nitrogen fixation / regulation of nitrogen utilization / phosphorelay response regulator activity / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP binding / cytoplasm
Similarity search - Function
DNA-binding transcriptional regulator NtrC / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain / Sigma-54 interaction domain profile. / RNA polymerase sigma factor 54 interaction domain ...DNA-binding transcriptional regulator NtrC / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain / Sigma-54 interaction domain profile. / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Response regulator receiver domain / cheY-homologous receiver domain / Response regulatory domain profile. / Signal transduction response regulator, receiver domain / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-binding transcriptional regulator NtrC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKern, D. / Volkman, B.F. / Luginbuhl, P. / Nohaile, M.J. / Kustu, S. / Wemmer, D.E.
Citation
Journal: Nature / Year: 1999
Title: Structure of a transiently phosphorylated switch in bacterial signal transduction.
Authors: Kern, D. / Volkman, B.F. / Luginbuhl, P. / Nohaile, M.J. / Kustu, S. / Wemmer, D.E.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Solution Structure of the N-Terminal Receiver Domain of NTRC
Authors: Volkman, B.F. / Nohaile, M.J. / Amy, N.K. / Kustu, S. / Wemmer, D.E.
History
DepositionNov 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITROGEN REGULATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,6371
Polymers13,6371
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)1 / -
Representativeclosest to the average

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Components

#1: Protein NITROGEN REGULATION PROTEIN / NTRC


Mass: 13636.604 Da / Num. of mol.: 1 / Fragment: N-TERMINAL RECEIVER DOMAIN(1-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P41789

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1223D 13C-SEPARATED NOESY
1332D NOESY

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Sample preparation

Details
Solution-IDContents
11 MM NTRC(1-124) U-15N; 50 MM SODIUM PHOSPHATE, PH 6.75
21 MM NTRC(1-124) U-15N/13C; 50 MM SODIUM PHOSPHATE, PH 6.75
31 MM NTRC(1-124) U-15N; 50 MM SODIUM PHOSPHATE, PH 6.75
Sample conditionsIonic strength: 50 mM / pH: 6.75 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5PETER GUENTERTstructure solution
Felix95MSIprocessing
XwinNMR1.5BRUKERcollection
DYANA1.5PETER GUENTERTdata analysis
XEASY1.3.13MUMENTHALERdata analysis
DYANA1.5PETER GUENTERTrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: STRUCTURE BASED ON A TOTAL OF 1768 UNIQUE DISTANCE CONSTRAINTS (OBTAINED FROM 3044 NOE CROSSPEAKS), INCLUDING 355 INTRARESIDUE, 464 SHORT-RANGE, 445 MEDIUM RANGE AND 504 LONG-RANGE ...Details: STRUCTURE BASED ON A TOTAL OF 1768 UNIQUE DISTANCE CONSTRAINTS (OBTAINED FROM 3044 NOE CROSSPEAKS), INCLUDING 355 INTRARESIDUE, 464 SHORT-RANGE, 445 MEDIUM RANGE AND 504 LONG-RANGE CONSTRAINTS. DYANA 1.5 ANNEAL COMMAND (10000 STEPS) USED TO GENERATE 40 CONFORMERS. 20 LOWEST TARGET FUNCTION STRUCTURES ANALYZED. CONFORMER 4 CHOSEN FOR DEPOSITION AS CLOSEST TO MEAN COORDINATES OF THE ENSEMBLE.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers submitted total number: 1

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