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- PDB-2jrl: Solution structure of the beryllofluoride-activated NtrC4 receive... -

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Basic information

Entry
Database: PDB / ID: 2jrl
TitleSolution structure of the beryllofluoride-activated NtrC4 receiver domain dimer
ComponentsTranscriptional regulator (NtrC family)
KeywordsTRANSCRIPTION / NTRC / NTRC4 / RECEIVER DOMAIN / TRANSCRIPTION REGULATOR / DIMER / Structural Genomics / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / 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 / Signal transduction response regulator, receiver domain ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / 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 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator (NtrC family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsTRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
AuthorsLee, C. / Hong, E. / Doucleff, M. / Pelton, J.G. / Wemmer, D.E. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: To be Published
Title: Solution Structure of the Beryllofluoride-Activated NtrC4 Receiver Domain Dimer.
Authors: Lee, C. / Doucleff, M. / Hong, E. / Pelton, J. / Wemmer, D.
History
DepositionJun 27, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator (NtrC family)
B: Transcriptional regulator (NtrC family)


Theoretical massNumber of molelcules
Total (without water)27,3332
Polymers27,3332
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)20 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulator (NtrC family)


Mass: 13666.570 Da / Num. of mol.: 2 / Fragment: NtrC4 receiver domain: Residues 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: ntrC4, aq_164 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66551

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: TRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1313D (H)CCH-TOCSY
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCA
17115N-IPAP-HSQC
182[F1] 13C-edited [F3] 13C-filtered HSQC-NOESY
191HBHA(CO)NH
11012D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] NtrC4Ra, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C] labeled, 0.8 mM non-labeled, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNtrC4Ra[U-100% 13C; U-100% 15N]1
0.8 mMlabeled[U-100% 13C]2
0.8 mMnon-labeled2
Sample conditionsIonic strength: 0 / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX9001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.1.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.12Goddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.1.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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