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- PDB-2lpm: Chemical Shift and Structure Assignments for Sma0114 -

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Basic information

Entry
Database: PDB / ID: 2lpm
TitleChemical Shift and Structure Assignments for Sma0114
ComponentsTwo-component response regulator
KeywordsTranscription regulator
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Two-component response regulator
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsSheftic, S.R. / Gage, D.J. / Alexandrescu, A.T.
CitationJournal: Biochemistry / Year: 2012
Title: Nuclear Magnetic Resonance Structure and Dynamics of the Response Regulator Sma0114 from Sinorhizobium meliloti.
Authors: Sheftic, S.R. / Garcia, P.P. / White, E. / Robinson, V.L. / Gage, D.J. / Alexandrescu, A.T.
History
DepositionFeb 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)13,6071
Polymers13,6071
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)20 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Two-component response regulator


Mass: 13606.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0058, SMa0114 / Production host: Escherichia coli (E. coli) / References: UniProt: Q930Y6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein, 1 mM DTT, 10 % 10% D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-100% 13C; U-100% 15N]1
1 mMDTT-21
10 %D2O-310%1
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: DGSA-distance geometry simulated annealing
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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