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- PDB-1p6u: NMR structure of the BeF3-activated structure of the response reg... -

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Basic information

Entry
Database: PDB / ID: 1p6u
TitleNMR structure of the BeF3-activated structure of the response regulator Chey2-Mg2+ from Sinorhizobium meliloti
ComponentsCheY2
KeywordsSIGNALING PROTEIN / CheY2 Beryllium fluoride / chemotaxis / response regulator / signal transduction / activation / Structural Proteomics in Europe / SPINE / Structural Genomics
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
Biological speciesSinorhizobium meliloti (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRiepl, H. / Scharf, B. / Maurer, T. / Schmitt, R. / Kalbitzer, H.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution Structures of the Inactive and BeF(3)-activated Response Regulator CheY2
Authors: Riepl, H. / Scharf, B. / Schmitt, R. / Kalbitzer, H.R. / Maurer, T.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: 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: CheY2


Theoretical massNumber of molelcules
Total (without water)13,7251
Polymers13,7251
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)16 / 250target function
RepresentativeModel #1lowest energy

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Components

#1: Protein CheY2


Mass: 13725.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q52884

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
171HNCA
181HNCO
191HN(CO)CA
1101CBCA(CO)CA
1111HBHA(CO)NH
1121(H)CCH-TOCSY
1131CC(CO)NH
NMR detailsText: TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1595, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 815, NUMBER OF SEQUENTIAL NOES USED FOR THE CALCULATION: 406, NUMBER OF MEDIUM RANGE ...Text: TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1595, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 815, NUMBER OF SEQUENTIAL NOES USED FOR THE CALCULATION: 406, NUMBER OF MEDIUM RANGE NOES USED FOR THE CALCULATION: 155, NUMBER OF LONG RANGE (I,J, J > I+4) NOES USED FOR THE CALCULATION: 219, NUMBER OF DIHEDRAL ANGLES RESTRAINTS USED FOR THE CALCULATION: 58, NUMBER OF HYDROGEN BOND RESTRAINTS USED FOR THE CALCULATION: 7, MINIMAL TARGET FUNCTION WAS 1.92, MEAN TARGET FUNCTION OF 16 STRUCTURES WAS 1.95 (+-0.2), THE NUMBER OF NOE VIOLATIONS > 0.02 NM WAS 5 (+-2), THE NUMBER OF NOE VIOLATIONS > 0.03 NM WAS 0, THE NUMBER OF DIHEDRAL ANGLES VIOLATIONS > 10 DEGREES WAS 0, RMSDS BACK BONE (6-124): 0.027 (+-0.007) NM, RMSDS ALL HEAVY ATOMS (6-124): 0.083 (+-0.013)NM

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Sample preparation

DetailsContents: 1mM CheY2, 1MM TRIS-HCL, 5MM MGCL2, 5MM BECL2, 50MM NAF
Solvent system: 5mM MgCl2, 20mM Tris/HCl
Sample conditionspH: 6.83 / Pressure: ambient / Temperature: 298 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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
AURELIA2.7.9Brukerdata analysis
DIANA1.5Guentertstructure solution
DIANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 250 / Conformers submitted total number: 16

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