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- PDB-2z33: Solution structure of the DNA complex of PhoB DNA-binding/transac... -

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Basic information

Entry
Database: PDB / ID: 2z33
TitleSolution structure of the DNA complex of PhoB DNA-binding/transactivation Domain
Components
  • 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'
  • 5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'
  • Phosphate regulon transcriptional regulatory protein phoB
KeywordsTRANSCRIPTION/DNA / WINGED HELIX-TURN-HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / phosphorelay response regulator 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
DNA / DNA (> 10) / Phosphate regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing molecluar dynamics
AuthorsYamane, T. / Okamura, H. / Ikeguchi, M. / Nishimura, Y. / Kidera, A.
CitationJournal: Proteins / Year: 2008
Title: Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment.
Authors: Yamane, T. / Okamura, H. / Ikeguchi, M. / Nishimura, Y. / Kidera, A.
History
DepositionMay 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'
C: 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'
A: Phosphate regulon transcriptional regulatory protein phoB


Theoretical massNumber of molelcules
Total (without water)21,9673
Polymers21,9673
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)10 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'


Mass: 4872.190 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'


Mass: 4921.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Phosphate regulon transcriptional regulatory protein phoB


Mass: 12173.898 Da / Num. of mol.: 1 / Fragment: residues 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoB / Plasmid: PT7-7-CB / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFJ5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D SEQUENTIAL ASSIGNMENT PROTOCOL
1213D HNHA
1314D 13C-SEPARATED NOESY
1414D 13C/15N-SEPARATED NOESY
1513D 15N-SEPARATED NOESY
1613D 13C SEPARATED NOESY, 2D NOESY
1712D TOCSY AND 2D COSY

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Sample preparation

DetailsContents: 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipedata analysis
PIPPdata analysis
CNS1A.BRUNGER et al.refinement
MARBLE0.3.46M.Ikeguchirefinement
RefinementMethod: simulated annealing molecluar dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2508 RESTRAINTS, 2263 ARE NOE-DERIVED DISTANCE RESTRAINTS 229 ARE DIHEDRAL ANGLE RESTRAINTS AND 16 ARE RESTRAINTS OF DNA BASE PLANALITY RESTRAINTS. ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2508 RESTRAINTS, 2263 ARE NOE-DERIVED DISTANCE RESTRAINTS 229 ARE DIHEDRAL ANGLE RESTRAINTS AND 16 ARE RESTRAINTS OF DNA BASE PLANALITY RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH CNS BY FOLLOWIN PROCEDURE. FIRST, ONLY THE STRUCTURES OF PROTEIN WERE CALCULATED USING THE HYBRID DISTANCE GEOMETRY-SIMULATED ANNEAING PROTOCOL WITH THE INTRA-PROTEIN RESTRAINTS, 10 OUT OF 100 CALCULATED STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATION GREATER THAN 2 DEGREES and A LOW TARGET ENERGY. SECOND, THE PROTEIN AND AN IDEALIZED B-FORM OF 16-MER DUPLEX DNA WERE DOCKED BY A SIMULATED ANNEALING PROTOCOL, FOR WHICH THE INTRA-DNA, INTER-MOLECULAR AND INTRA-PROTEIN RESTRAINTS WERE EMPLOYED. AS AN INITIAL STRUCTURE, EACH OF THE 10 PROTEIN STRUCTURES WAS PLACED IN 15 DIFFERENT POSITIONS 50 ANGSTROMS AWAY FROM THE DNA. NEXT, EACH OF THE 150 DOCKED COMPLEX STRUCTURES WAS FURTHER REFINED BY A SIMULATED ANNEALING PROTOCOL. FINALLY, 20 STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 ANGSTROME AND NO TORSION ANGLE VIOLATION THAN 2 DEGREES AND A LOW TARGET ENERGY. ADDITIONALLY, 10 CNS-SELECTED STRUCTURES WERE REFINED IN REALISTIC SOLUTION SISTEM BY USING MOLECULAR DYNAMICS SIMULATION PROGRAM, MARBLE WITH RESTRAINT FUNCTIONS FOR NOE DISTANCE DIHEDRAL ANGLE AND PLANARITY OF DNA BASE PAIR USED IN CNS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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