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- PDB-2n9u: Solution NMR structure of Erythrobacter litoralis PhyR response r... -

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Basic information

Entry
Database: PDB / ID: 2n9u
TitleSolution NMR structure of Erythrobacter litoralis PhyR response regulator REC domain
ComponentsResponse regulator
KeywordsTRANSCRIPTION / Response Regulator / Receiver / Two-component signaling
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / : / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / : / 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
Biological speciesErythrobacter litoralis HTCC2594 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsCorrea, F. / Gardner, K.H.
CitationJournal: Cell Chem Biol / Year: 2016
Title: Basis of Mutual Domain Inhibition in a Bacterial Response Regulator.
Authors: Correa, F. / Gardner, K.H.
History
DepositionDec 9, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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_software.name / _struct_ref_seq_dif.details
Revision 1.4May 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: Response regulator


Theoretical massNumber of molelcules
Total (without water)13,8241
Polymers13,8241
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Response regulator


Mass: 13823.528 Da / Num. of mol.: 1 / Fragment: Response regulatory domain, residues 142-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter litoralis HTCC2594 (bacteria)
Strain: HTCC2594 / Gene: ELI_10215 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2N856

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5-1 mM [U-99% 13C; U-99% 15N] protein, 10 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-99% 13C; U-99% 15N]0.5-11
10 mMTRIS-21
50 mMsodium chloride-31
Sample conditionsIonic strength: 0.05 / pH: 7 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
VnmrJVariancollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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