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- PDB-1f62: WSTF-PHD -

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Basic information

Entry
Database: PDB / ID: 1f62
TitleWSTF-PHD
ComponentsTRANSCRIPTION FACTOR WSTF
KeywordsTRANSCRIPTION / Zn-finger
Function / homology
Function and homology information


histone H2AXY142 kinase activity / WICH complex / negative regulation of mitotic chromosome condensation / histone kinase activity / B-WICH complex / : / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / pericentric heterochromatin / condensed chromosome ...histone H2AXY142 kinase activity / WICH complex / negative regulation of mitotic chromosome condensation / histone kinase activity / B-WICH complex / : / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / pericentric heterochromatin / condensed chromosome / post-translational protein modification / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / B-WICH complex positively regulates rRNA expression / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone binding / chromatin remodeling / phosphorylation / DNA damage response / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Tyrosine-protein kinase BAZ1B, bromodomain / : / : / WSTF/Acf1/Cbp146 / ATP-utilising chromatin assembly and remodelling N-terminal / WAC domain profile. / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DDT domain / WHIM2 domain ...Tyrosine-protein kinase BAZ1B, bromodomain / : / : / WSTF/Acf1/Cbp146 / ATP-utilising chromatin assembly and remodelling N-terminal / WAC domain profile. / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase BAZ1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Restrained molecular dynamics using AMBER-6 program
AuthorsPascual, J. / Martinez-Yamout, M. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor.
Authors: Pascual, J. / Martinez-Yamout, M. / Dyson, H.J. / Wright, P.E.
History
DepositionJun 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_related.db_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR WSTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9543
Polymers5,8231
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #17lowest energy

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Components

#1: Protein TRANSCRIPTION FACTOR WSTF


Mass: 5822.804 Da / Num. of mol.: 1 / Fragment: PHD ZINC FINGER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UIG0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1mM WSTF-PHD U-15N,13C; / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglioprocessing
DYANA1Guntertstructure solution
DYANA1Guntertrefinement
RefinementMethod: Restrained molecular dynamics using AMBER-6 program / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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