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- PDB-1kkx: Solution structure of the DNA-binding domain of ADR6 -

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Basic information

Entry
Database: PDB / ID: 1kkx
TitleSolution structure of the DNA-binding domain of ADR6
ComponentsTranscription regulatory protein ADR6
KeywordsDNA BINDING PROTEIN / ARID / ADR6 / DNA-binding domain
Function / homology
Function and homology information


positive regulation of mating type switching / HDACs deacetylate histones / SWI/SNF complex / cellular response to amino acid starvation / DNA-templated DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin ...positive regulation of mating type switching / HDACs deacetylate histones / SWI/SNF complex / cellular response to amino acid starvation / DNA-templated DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
ARID DNA-binding domain / : / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SWI/SNF chromatin-remodeling complex subunit SWI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTu, X. / Wu, J. / Xu, Y. / Shi, Y.
Citation
Journal: J.Biomol.Nmr / Year: 2001
Title: 1H, 13C and 15N resonance assignments and secondary structure of ADR6 DNA-binding domain.
Authors: Tu, X. / Wu, J. / Xu, Y. / Shi, Y.
#1: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H, 13C and 15N resonance assignments and secondary structure of ADR6 DNA-binding domain
Authors: Tu, X. / Wu, J. / Xu, Y. / Shi, Y.
#2: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2000
Title: Expression and purification of a recombinant DNA-binding domain of ADR6 protein from Escherichia coli and its secondary structure characterization
Authors: Tu, X. / Xiao, Y. / Zeng, W. / Shi, Y.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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
A: Transcription regulatory protein ADR6


Theoretical massNumber of molelcules
Total (without water)14,5671
Polymers14,5671
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)10 / 100structures with the lowest energy
Representative

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Components

#1: Protein Transcription regulatory protein ADR6 / Transcription regulatory protein SWI1


Mass: 14566.800 Da / Num. of mol.: 1 / Fragment: ARID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: adr6 / Plasmid: pREP-4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09547

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
3332D NOESY

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Sample preparation

DetailsContents: 1mM ADR6 ARID domain U-15N, U-13C, 50mM phosphate buffer at pH4.9, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 4.9 / Pressure: ambient / Temperature: 300 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 spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Version: v 1.0 / Developer: A.T. Brunger / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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