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- PDB-2glo: Solution structure of the Brinker DNA binding domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 2glo
TitleSolution structure of the Brinker DNA binding domain in complex with the omb enhancer
Components
  • 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'
  • 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'
  • brinker CG9653-PA
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / HELIX-TURN-HELIX MOTIF / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


posterior Malpighian tubule development / wing disc morphogenesis / cell competition in a multicellular organism / imaginal disc-derived wing morphogenesis / negative regulation of BMP signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / nucleic acid binding / negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brinker DNA-binding domain / Brinker DNA-binding domain / : / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Brinker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics; distance geometry
AuthorsCordier, F. / Hartmann, B. / Rogowski, M. / Affolter, M. / Grzesiek, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: DNA recognition by the brinker repressor - an extreme case of coupling between binding and folding
Authors: Cordier, F. / Hartmann, B. / Rogowski, M. / Affolter, M. / Grzesiek, S.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 29, 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
B: 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'
C: 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'
A: brinker CG9653-PA


Theoretical massNumber of molelcules
Total (without water)14,3883
Polymers14,3883
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3' / DNA OPTOMOTOR BLIND (OMB) ENHANCER


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3' / DNA OPTOMOTOR BLIND (OMB) ENHANCER


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein brinker CG9653-PA / BRINKER NUCLEAR REPRESSOR


Mass: 7061.949 Da / Num. of mol.: 1 / Fragment: Brinker DNA binding domain (residues 43-101)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: brinker / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XTN4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1313D dq-HNHA
1423D dq-HAHB, 2D HNCG, 2D HN(CO)CG
1522D 13C-selected/12C,14N-selected NOESY
163DSSE, J-MODULATED-13C-HSQC
NMR detailsText: This structure was determined using standard 2D and 3D heteronuclear techniques and 12C/14N-filtered-NOESY experiments for DNA assignment and intermolecular NOE contacts

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM brkDBD U-15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O95% H2O/5% D2O
21mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O95% H2O/5% D2O
30.35mM brkDBD U-13C/15N, 0.35mM DNA omb12 NA; 10mM NaCl; 20mM potassium phosphate; 2mM DTT; 0.02% NaN3; 25mg/ml Pf1-phages; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 10mM NaCl / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.2Delaglioprocessing
PIPP4.3.2Garrettdata analysis
HADDOCK1.2Bonvinrefinement
RefinementMethod: torsion angle dynamics; distance geometry / Software ordinal: 1
Details: The structures are based on 1279 NOE-derived distance constraints, 21 Ambiguous Interaction Restraints, 21 distance restraints from hydrogen bonds, 92 RDC restraints, 30 dihedral angle ...Details: The structures are based on 1279 NOE-derived distance constraints, 21 Ambiguous Interaction Restraints, 21 distance restraints from hydrogen bonds, 92 RDC restraints, 30 dihedral angle restraints, 56 J-coupling constant restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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