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- PDB-1j56: MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC REC... -

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Entry
Database: PDB / ID: 1j56
TitleMINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS
ComponentsNITROGEN REGULATION PROTEIN NR(I)
KeywordsSIGNALING PROTEIN / two component signal transduction / receiver domain / BeF3 / phosphorylation / Bacterial nitrogen regulatory protein
Function / homology
Function and homology information


regulation of nitrogen utilization / nitrogen fixation / phosphorelay response regulator activity / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / 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 site 2 / Sigma-54 interaction domain ATP-binding region B 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 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 site 2 / Sigma-54 interaction domain ATP-binding region B 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / DNA-binding transcriptional regulator NtrC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, simulated annealing, ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsHastings, C.A. / Lee, S.-Y. / Cho, H.S. / Yan, D. / Kustu, S. / Wemmer, D.E.
Citation
Journal: Biochemistry / Year: 2003
Title: High-Resolution Solution Structure of the Beryllofluoride-Activated NtrC Receiver Domain
Authors: Hastings, C.A. / Lee, S.-Y. / Cho, H.S. / Yan, D. / Kustu, S. / Wemmer, D.E.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: NMR STRUCTURE OF ACTIVATED CHEY
Authors: Cho, H.S. / Lee, S.-Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G.
#2: Journal: Nat.Struct.Biol. / Year: 2001
Title: CRYSTAL STRUCTURE OF AN ACTIVATED RESPONSE REGULATOR BOUND TO ITS TARGET
Authors: Lee, S.-Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D.S. / Huang, L. / Kustu, S. / Berry, E.A. / Wemmer, D.E.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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: NITROGEN REGULATION PROTEIN NR(I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7032
Polymers13,6371
Non-polymers661
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 / -
Representativeminimized average structure

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Components

#1: Protein NITROGEN REGULATION PROTEIN NR(I)


Mass: 13636.604 Da / Num. of mol.: 1
Fragment: N-terminal domain: Receiver domain, Residues 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P41789
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2224D 13C/15N-separated NOESY
2324D 13C-separated NOESY
2423D 13C-separated NOESY
252HNCA-J
262CBCA(CO)NH
37313C,1H-HSQC
484IPAP-HSQC
292HNHA
NMR detailsText: MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE 3 SITE CONTACTS.

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N; 1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O95% H2O/5% D2O
2U-15N, 13C;1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O95% H2O/5% D2O
310% 13C;1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O95% H2O/5% D2O
4U-15N; 1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O; 30mg/ml phage pf195% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75 ambient 303 K
250mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75 ambient 303 K
350mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75 ambient 303 K
450mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertstructure solution
CNS 1.0Brungerstructure solution
Felixprocessing
NMRViewJohnsondata analysis
CNS 1.0Brunger et. al.refinement
MOLMOLrefinement
RefinementMethod: distance geometry, torsion angle dynamics, simulated annealing, ENERGY MINIMIZATION
Software ordinal: 1
Details: 3 additional constraints from crystal structure of BeF3-activated CheY were used for structure calculation.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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