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- PDB-1umq: solution structure and DNA binding of the effector domain from th... -

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Basic information

Entry
Database: PDB / ID: 1umq
Titlesolution structure and DNA binding of the effector domain from the global regulator PrrA(RegA) from R. sphaeroides: Insights into DNA binding specificity
ComponentsPHOTOSYNTHETIC APPARATUS REGULATORY PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / RESPONSE REGULATOR / DNA BINDING DOMAIN / HELIX-TURN-HELIX / SENSORY TRANSDUCTION / PHOSPHORYLATION / TRANSCRIPTION REGULATION / DNA-BINDING / ACTIVATOR
Function / homology
Function and homology information


phosphorelay signal transduction system / DNA binding
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Photosynthetic apparatus regulatory protein RegA
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodSOLUTION NMR / DISTANCE, DIHEDRAL RESTRAINTS (TALOS)
AuthorsLaguri, C. / Phillips-Jones, M.K. / Williamson, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Solution Structure and DNA Binding of the Effector Domain from the Global Regulator Prra(Rega) from Rhodobacter Sphaeroides: Insights Into DNA Binding Specificity
Authors: Laguri, C. / Phillips-Jones, M.K. / Williamson, M.P.
History
DepositionAug 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOTOSYNTHETIC APPARATUS REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,4831
Polymers9,4831
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)5 / 20RANDOM
RepresentativeModel #1

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Components

#1: Protein PHOTOSYNTHETIC APPARATUS REGULATORY PROTEIN / REGA / REGA PROTEIN / RESPONSE REGULATOR / PRRA


Mass: 9482.878 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN, RESIDUES 125-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53228
Compound detailsINVOLVED IN TRANSACTIVATING ANAEROBIC EXPRESSION OF THE PHOTOSYNTHETIC APPARATUS. IT IS A ...INVOLVED IN TRANSACTIVATING ANAEROBIC EXPRESSION OF THE PHOTOSYNTHETIC APPARATUS. IT IS A TRANSCRIPTIONAL REGULATOR THAT IS RESPONSIBLE FOR ACTIVATING EXPRESSION OF THE PUF, PUH, AND PUC OPERONS IN RESPONSE TO A DECREASE IN OXYGEN TENSION. THIS ENTRY CORRESPONDS TO RESIDUES 125 THROUGH 184 OF THE INTACT PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-15N EDITED NOESY
121CBCA(CO)NH
131HNCA
141HN(CA)CB
151HNCO
161HN(CA)CO
171(H)CCH
181CCH TOCSY
19113C
110115N HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PRRA C-TERMINAL DOMAIN

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Sample preparation

Sample conditionsIonic strength: 0.6 / pH: 6.0 / Pressure: 1 atm / Temperature: 275 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2LINGE ET AL 2003refinement
ARIA1.2structure solution
RefinementMethod: DISTANCE, DIHEDRAL RESTRAINTS (TALOS) / Software ordinal: 1
Details: REFINEMENT IN EXPLICIT WATER AS DESCRIBED IN THE REFERENCE ABOVE
NMR ensembleConformer selection criteria: RANDOM / Conformers calculated total number: 20 / Conformers submitted total number: 5

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