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Basic information

Entry
Database: PDB / ID: 1yqa
TitleEngineering the structural stability and functional properties of the GI domain into the intrinsically unfolded GII domain of the yeast linker histone Hho1p
ComponentsHistone H1
KeywordsDNA BINDING PROTEIN / Winged-helix
Function / homology
Function and homology information


negative regulation of DNA recombination / supercoiled DNA binding / chromosome condensation / phosphate ion binding / nucleosomal DNA binding / protein-DNA complex / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly ...negative regulation of DNA recombination / supercoiled DNA binding / chromosome condensation / phosphate ion binding / nucleosomal DNA binding / protein-DNA complex / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / double-stranded DNA binding / nucleic acid binding / molecular adaptor activity / regulation of DNA-templated transcription / chromatin / DNA binding / nucleus
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / see journal citation
AuthorsSanderson, A. / Stott, K. / Stevens, T.J. / Thomas, J.O.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Engineering the Structural Stability and Functional Properties of the GI Domain into the Intrinsically Unfolded GII Domain of the Yeast Linker Histone Hho1p.
Authors: Sanderson, A. / Stott, K. / Stevens, T.J. / Thomas, J.O.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Two homologous domains of similar structure but different stability in the yeast linker histone, Hho1p
Authors: Ali, T. / Coles, P. / Stevens, T.J. / Stott, K. / Thomas, J.O.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Histone H1


Theoretical massNumber of molelcules
Total (without water)9,5531
Polymers9,5531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone H1


Mass: 9553.217 Da / Num. of mol.: 1 / Fragment: GII loop mutant (GII-L), Residues 171-258
Mutation: F210Y, S211P, delta-S212, K213I, L214V, K215G, T216S, S217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HHO1 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53551

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM GII-L U-15N,13C; 100mM phosphate buffer; 1mM EDTA; 1-2mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate / pH: 7.0 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRcollection
Azara2.7processing
Analysis1Boucher, W. & Stevens, T.J.data analysis
ARIA1.1.2structure solution
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: see journal citation / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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