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- PDB-1uhm: Solution structure of the globular domain of linker histone homol... -

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Basic information

Entry
Database: PDB / ID: 1uhm
TitleSolution structure of the globular domain of linker histone homolog Hho1p from S. cerevisiae
ComponentsHistone H1
KeywordsSTRUCTURAL PROTEIN / winged helix-turn-helix / linker histone / S. cerevisiae / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


sporulation / negative regulation of DNA recombination / regulation of double-strand break repair / supercoiled DNA binding / chromosome condensation / nucleosomal DNA binding / phosphate ion binding / protein-DNA complex / chromatin DNA binding / nucleosome assembly ...sporulation / negative regulation of DNA recombination / regulation of double-strand break repair / supercoiled DNA binding / chromosome condensation / nucleosomal DNA binding / phosphate ion binding / protein-DNA complex / chromatin DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / double-stranded DNA binding / molecular adaptor activity / nucleic acid binding / 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 / distance geometry simulated annealing, molecular dynamics
AuthorsOno, K. / Kusano, O. / Shimotakahara, S. / Shimizu, M. / Yamazaki, T. / Shindo, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy.
Authors: Ono, K. / Kusano, O. / Shimotakahara, S. / Shimizu, M. / Yamazaki, T. / Shindo, H.
History
DepositionJul 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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)8,5171
Polymers8,5171
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 / 100structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: Protein Histone H1 / Histone Hho1p


Mass: 8516.781 Da / Num. of mol.: 1 / Fragment: globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HHO1 / Plasmid: pET21b / 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

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Sample preparation

DetailsContents: 1mM HD1 U-15N,13C; 10mM phosphate buffer / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.2 / Pressure: ambient / Temperature: 298 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: 750 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger, A.T. / Classification: refinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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