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- PDB-2li6: 1H, 13C, and 15N Chemical Shift Assignments for yeast protein -

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Basic information

Entry
Database: PDB / ID: 2li6
Title1H, 13C, and 15N Chemical Shift Assignments for yeast protein
ComponentsSWI/SNF chromatin-remodeling complex subunit SWI1
KeywordsDNA BINDING PROTEIN / Ligand binding
Function / homology
Function and homology information


carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of mating type switching / HDACs deacetylate histones / SWI/SNF complex / DNA-templated DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II ...carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of mating type switching / HDACs deacetylate histones / SWI/SNF complex / DNA-templated DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
ARID DNA-binding domain / ARID/BRIGHT 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 / 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 / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsWang, T. / Zhang, J. / Tu, X.
CitationJournal: Proteins / Year: 2012
Title: Solution structure of SWI1 ARID domain from Saccharomyces cerevisiae and its non-specific binding to DNA
Authors: Wang, T. / Zhang, J. / Zhang, X. / Tu, X.
History
DepositionAug 24, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SWI/SNF chromatin-remodeling complex subunit SWI1


Theoretical massNumber of molelcules
Total (without water)13,8191
Polymers13,8191
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)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein SWI/SNF chromatin-remodeling complex subunit SWI1 / Regulatory protein GAM3 / SWI/SNF complex subunit SWI1 / Transcription regulatory protein ADR6 / ...Regulatory protein GAM3 / SWI/SNF complex subunit SWI1 / Transcription regulatory protein ADR6 / Transcription regulatory protein SWI1


Mass: 13818.961 Da / Num. of mol.: 1 / Fragment: UNP residues 390-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ADR6, GAM3, SWI1, YPL016W, LPA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09547

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D H(CCO)NH
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D C(CO)NH

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Sample preparation

DetailsContents: 100 mM sodium chloride-1, 2 mM sodium phosphate-2, 1.5 mM EDTA-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium chloride-11
2 mMsodium phosphate-21
1.5 mMEDTA-31
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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