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- PDB-2msl: Solution Structure and Chemical Shift Assignments for the Apo for... -

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Basic information

Entry
Database: PDB / ID: 2msl
TitleSolution Structure and Chemical Shift Assignments for the Apo form of the Receiver Domain of Nitrogen Regulatory Protein C (NTRC) at 35C
ComponentsNitrogen regulation protein NR(I)
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of nitrogen utilization / nitrogen fixation / phosphorelay response regulator activity / phosphorelay signal transduction system / 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 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
Nitrogen regulation protein NR(I) / DNA-binding transcriptional regulator NtrC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsClarkson, M.W. / Pontiggia, F. / Villali, J. / Kern, D.
CitationJournal: Nat Commun / Year: 2015
Title: Free energy landscape of activation in a signalling protein at atomic resolution.
Authors: Pontiggia, F. / Pachov, D.V. / Clarkson, M.W. / Villali, J. / Hagan, M.F. / Pande, V.S. / Kern, D.
History
DepositionAug 4, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulation protein NR(I)


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)25 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nitrogen regulation protein NR(I)


Mass: 13636.604 Da / Num. of mol.: 1 / Fragment: UNP residues 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: ATCC 68169 / UK-1 / Gene: glnG ntrC STM4005 / Plasmid: pET-7 / Production host: Escherichia coli (E. coli) / References: UniProt: F5ZY36, UniProt: A0A0M3KKS6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1713D (H)CCH-TOCSY
1813D HCCH3-TOCSY
1912D (HB)CB(CGCD)HD
11012D (HB)CB(CGCDCE)HE
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D 1H-13C HSQC aliphatic
11512D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] Receiver Domain of NtrC, 50 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMReceiver Domain of NtrC-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
Sample conditionsIonic strength: 50 / pH: 6.75 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent INOVAAgilentINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CARAWuthrich, K. et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 25

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