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- PDB-5j8j: A histone deacetylase from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5j8j
TitleA histone deacetylase from Saccharomyces cerevisiae
ComponentsHistone deacetylase HDA1
KeywordsHYDROLASE / Rossmann fold / deacetylase
Function / homology
Function and homology information


HDA1 complex / HSF1 activation / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
Histone deacetylase class II, yeast / Arb2 domain / Arb2-like domain / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Histone deacetylase HDA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.716 Å
AuthorsZhu, Y. / Shen, H. / Li, X. / Teng, M.
CitationJournal: Sci Rep / Year: 2016
Title: Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae.
Authors: Shen, H. / Zhu, Y. / Wang, C. / Yan, H. / Teng, M. / Li, X.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase HDA1


Theoretical massNumber of molelcules
Total (without water)28,8861
Polymers28,8861
Non-polymers00
Water00
1
A: Histone deacetylase HDA1

A: Histone deacetylase HDA1


Theoretical massNumber of molelcules
Total (without water)57,7712
Polymers57,7712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3390 Å2
ΔGint-27 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.974, 104.974, 86.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Histone deacetylase HDA1


Mass: 28885.723 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 457-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HDA1, YNL021W, N2819 / Production host: Escherichia coli (E. coli) / References: UniProt: P53973, histone deacetylase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14972 / % possible obs: 98.1 % / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.7
Reflection shellRedundancy: 10.3 % / Mean I/σ(I) obs: 3.1 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.716→40.284 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.82
RfactorNum. reflection% reflection
Rfree0.2382 781 5.23 %
Rwork0.1898 --
obs0.1922 14934 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.716→40.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 0 1917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091979
X-RAY DIFFRACTIONf_angle_d1.2812698
X-RAY DIFFRACTIONf_dihedral_angle_d13.9696
X-RAY DIFFRACTIONf_chiral_restr0.049312
X-RAY DIFFRACTIONf_plane_restr0.006343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.716-2.88610.35461190.27982260X-RAY DIFFRACTION95
2.8861-3.10890.34081350.25572334X-RAY DIFFRACTION98
3.1089-3.42160.31641360.22822338X-RAY DIFFRACTION98
3.4216-3.91640.26221370.19182358X-RAY DIFFRACTION99
3.9164-4.93280.20061310.17062407X-RAY DIFFRACTION99
4.9328-40.28850.2091230.17462456X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -46.2438 Å / Origin y: 18.2399 Å / Origin z: -25.4993 Å
111213212223313233
T0.8134 Å2-0.0211 Å20.1091 Å2-0.7455 Å20.0487 Å2--0.8099 Å2
L0.8873 °2-0.7118 °21.0061 °2-2.5034 °2-0.2788 °2--2.5582 °2
S0.1827 Å °0.038 Å °-0.0494 Å °-0.1766 Å °-0.096 Å °-0.0876 Å °-0.0447 Å °0.2345 Å °-0.044 Å °
Refinement TLS groupSelection details: all

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