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- PDB-3hgq: Structural and functional studies of the yeast class II Hda1 HDAC... -

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Basic information

Entry
Database: PDB / ID: 3hgq
TitleStructural and functional studies of the yeast class II Hda1 HDAC complex
ComponentsHDA1 complex subunit 3
KeywordsTRANSCRIPTION / RecA-like domain / SWI2/SNF2 helical domain / Chromatin regulator / Coiled coil / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


HDA1 complex / regulatory ncRNA-mediated gene silencing / chromosome segregation / chromatin remodeling / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol
Similarity search - Function
Rossmann fold - #12360 / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Class II histone deacetylase complex subunits 2 and 3 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HDA1 complex subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsLee, J.H. / Maskos, K. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and Functional Studies of the Yeast Class II Hda1 Histone Deacetylase Complex.
Authors: Lee, J.H. / Maskos, K. / Huber, R.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HDA1 complex subunit 3
B: HDA1 complex subunit 3
C: HDA1 complex subunit 3
D: HDA1 complex subunit 3


Theoretical massNumber of molelcules
Total (without water)152,5514
Polymers152,5514
Non-polymers00
Water00
1
A: HDA1 complex subunit 3
B: HDA1 complex subunit 3


Theoretical massNumber of molelcules
Total (without water)76,2752
Polymers76,2752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area27720 Å2
MethodPISA
2
C: HDA1 complex subunit 3
D: HDA1 complex subunit 3


Theoretical massNumber of molelcules
Total (without water)76,2752
Polymers76,2752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.080, 132.580, 90.170
Angle α, β, γ (deg.)90.00, 92.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 27:166 or resseq 173:223 or resseq 230:328 )
211chain B and (resseq 27:166 or resseq 173:223 or resseq 230:328 )
311chain C and (resseq 27:166 or resseq 173:223 or resseq 230:328 )
411chain D and (resseq 27:166 or resseq 173:223 or resseq 230:328 )

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Components

#1: Protein
HDA1 complex subunit 3 / scHda3pDBD3 / Histone deacetylase complex 1 subunit 3


Mass: 38137.641 Da / Num. of mol.: 4 / Fragment: UNP residues 6-333 / Mutation: K168A, Q169A, K170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HDA3, PLO1, YPR179C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06623
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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97815, 0.97876, 0.97469
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2008
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978151
20.978761
30.974691
ReflectionResolution: 3→30 Å / Num. obs: 28294 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.126
Reflection shellResolution: 3→3.12 Å / Rsym value: 0.545 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→19.872 Å / SU ML: 0.44 / σ(F): 1.37 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 1410 5 %random
Rwork0.224 ---
all0.2267 28294 --
obs0.2267 28181 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.656 Å2 / ksol: 0.302 e/Å3
Refinement stepCycle: LAST / Resolution: 3→19.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 0 0 9552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059777
X-RAY DIFFRACTIONf_angle_d0.90413269
X-RAY DIFFRACTIONf_dihedral_angle_d17.6883594
X-RAY DIFFRACTIONf_chiral_restr0.0611518
X-RAY DIFFRACTIONf_plane_restr0.0031656
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2373X-RAY DIFFRACTIONPOSITIONAL
12B2373X-RAY DIFFRACTIONPOSITIONAL0.031
13C2373X-RAY DIFFRACTIONPOSITIONAL0.029
14D2373X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.10680.39631400.3162665100
3.1068-3.23070.36751390.28032647100
3.2307-3.3770.31531420.25092682100
3.377-3.55410.26281410.23532678100
3.5541-3.77540.28411410.21422677100
3.7754-4.06460.27061400.19822660100
4.0646-4.46940.22591400.18642675100
4.4694-5.10660.22931420.17472696100
5.1066-6.39790.27341410.21132684100
6.3979-19.87230.22131440.1978270799

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