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- PDB-1zit: Structure of the receiver domain of NtrC4 from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 1zit
TitleStructure of the receiver domain of NtrC4 from Aquifex aeolicus
Componentstranscriptional regulator (NtrC family)
KeywordsTRANSCRIPTION REGULATOR / (beta/alpha)5
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 / simulated annealing
AuthorsMatsubara, K. / Pelton, J.G. / Wemmer, D.E.
CitationJournal: To be Published
Title: Structure and consequences of activiation of the receiver domain of NtrC4 from Aquifex aeolicus
Authors: Matsubara, K. / Pelton, J.G. / Wemmer, D.E.
History
DepositionApr 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
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: transcriptional regulator (NtrC family)


Theoretical massNumber of molelcules
Total (without water)13,6671
Polymers13,6671
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)38 / 100structures with favorable non-bond energy
RepresentativeModel #11lowest energy

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Components

#1: Protein transcriptional regulator (NtrC family)


Mass: 13666.570 Da / Num. of mol.: 1 / Fragment: receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: AQ_164 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O66551

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
1412D NOESY
15115N-IPAP-HSQC

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Sample preparation

DetailsContents: 1mM NtrC4r U-15N,13C 10 mM phosphate buffer pH 7.0.
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 40 mM / pH: 7 / Pressure: ambient / Temperature: 323 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
NMRPipeLinuxDelaglioprocessing
NMRView5Johnsondata analysis
DYANA1.5Guntertstructure solution
DYANA1.5Guntertrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 1155 NOE restraints, 19 hydrogen bonds (38 restraints), 57 Phi dihedral restraints, 11 Chi1 restraints, and 24 1H-15N residual dipolar coupling restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 38

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