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- PDB-1qqi: SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1qqi
TitleSOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI
ComponentsPHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
KeywordsTRANSCRIPTION / WINGED HELIX-TURN-HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / phosphorelay response regulator activity / DNA-binding transcription activator activity / regulation of DNA-templated transcription initiation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphate regulon transcriptional regulatory protein PhoB / Phosphate regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / 4D SIMULATED ANNEALING
AuthorsOkamura, H. / Hanaoka, S. / Nagadoi, A. / Makino, K. / Nishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box.
Authors: Okamura, H. / Hanaoka, S. / Nagadoi, A. / Makino, K. / Nishimura, Y.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Theoretical massNumber of molelcules
Total (without water)12,1741
Polymers12,1741
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)1 / -
Representative

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Components

#1: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Mass: 12173.898 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-7-CB / Production host: Escherichia coli (E. coli) / References: UniProt: P08402, UniProt: P0AFJ5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1213D 13C-SEPARATED NOESY
1323D 15N-SEPARATED NOESY
1414D 13C-SEPARATED NOESY
152HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
11-2MM PROTEIN U-15N,13C; 50MM PHOSPHATE BUFFER, 500MM NACL
21-2MM PROTEIN U-15N; 50MM PHOSPHATE BUFFER, 500MM NACL
31-2MM PROTEIN ; 50MM PHOSPHATE BUFFER, 500MM NACL
Sample conditionsIonic strength: NACL 500mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.6DELAGLIO, F.structure solution
PIPP3.9GARRETT, D.S.structure solution
EMBOSS5NAKAI,T., KIDERA, A. AND NAKAMURA, H.refinement
RefinementMethod: 4D SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1758 RESTRAINTS, 1719 ARE NOE-DERIVED DISTANCE RESTRAINTS AND 39 DIHEDRAL ANGLE RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH EMBOSS BY USING ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1758 RESTRAINTS, 1719 ARE NOE-DERIVED DISTANCE RESTRAINTS AND 39 DIHEDRAL ANGLE RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH EMBOSS BY USING A 4D SIMULATED ANNEALING PROTOCOL STARTING FROM A RANDOM COIL CONFORMATION. THE GENERATED STRUCTURES WERE FURTHER REFINED BY ENERGY MINIMIZATION USING THE AMBER FORCE FIELD. THE FINAL STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATIONS GREATER THAN 0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEGREES, AND A LOW TARGET ENERGY.
NMR ensembleConformers submitted total number: 1

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