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- PDB-1jxs: Solution Structure of the DNA-Binding Domain of Interleukin Enhan... -

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Basic information

Entry
Database: PDB / ID: 1jxs
TitleSolution Structure of the DNA-Binding Domain of Interleukin Enhancer Binding Factor
Componentsinterleukin enhancer binding factor
KeywordsDNA BINDING PROTEIN / DNA-BINDING DOMAIN / WINGED HELIX
Function / homology
Function and homology information


canonical glycolysis / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / negative regulation of autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding ...canonical glycolysis / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / negative regulation of autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
: / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...: / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Forkhead box protein K2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Hybrid distance geometry-dynamical simulated annealing method
AuthorsChuang, W.J. / Liu, P.P. / Li, C. / Hsieh, Y.H. / Chen, S.W. / Chen, S.H. / Jeng, W.Y.
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2002
Title: Solution structure of the DNA-binding domain of interleukin enhancer binding factor 1 (FOXK1a)
Authors: Liu, P.P. / Chen, Y.C. / Li, C. / Hsieh, Y.H. / Chen, S.W. / Chen, S.H. / Jeng, W.Y. / Chuang, W.J.
History
DepositionSep 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2003Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: interleukin enhancer binding factor


Theoretical massNumber of molelcules
Total (without water)11,5621
Polymers11,5621
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 / 50all calculated structures submitted
RepresentativeModel #20fewest violations

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Components

#1: Protein interleukin enhancer binding factor / ILF-1


Mass: 11562.141 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILF-1 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q01167

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
3433D 15N-separated NOESY
3533D 15N-separated NOESY
4643D 13C-separated NOESY
NMR detailsText: HNCA, HN(CO)CA, HNCBCA, CBCA(CO)NH, HBHA(CBCA)NH, HBHA(CBCACO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM ILF, 25mM phosphate buffer, 100mM NaCl90% H2O/10% D2O
23mM ILF, 25mM phosphate buffer, 100mM NaCl100% D2O
33mM ILF U-15N, 25mM phosphate buffer, 100mM NaCl90% H2O/10% D2O
42mM ILF U-15N, 13C, 25mM phosphate buffer, 100mM NaCl90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11256ambient 300 K
21256ambient 300 K
31256ambient 300 K
41256ambient 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85refinement
AURELIA2.7.10Neidigdata analysis
XwinNMR2.6Brukerprocessing
RefinementMethod: Hybrid distance geometry-dynamical simulated annealing method
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 20

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