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- PDB-5ikk: Structure of the histone deacetylase Clr3 -

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Basic information

Entry
Database: PDB / ID: 5ikk
TitleStructure of the histone deacetylase Clr3
ComponentsHistone deacetylase clr3
KeywordsTRANSCRIPTION / hdac domain / alpha/beta hydrolase domain / dimer / alpha/beta sandwich / Hydrolase
Function / homology
Function and homology information


Cilium Assembly / HSF1 activation / SHREC complex / : / : / histone H3K14 deacetylase activity / positive regulation of pericentric heterochromatin formation / HDACs deacetylate histones / NAD-dependent histone H3K14 deacetylase activity / SUMOylation of chromatin organization proteins ...Cilium Assembly / HSF1 activation / SHREC complex / : / : / histone H3K14 deacetylase activity / positive regulation of pericentric heterochromatin formation / HDACs deacetylate histones / NAD-dependent histone H3K14 deacetylase activity / SUMOylation of chromatin organization proteins / : / mating-type region heterochromatin / heterochromatin island / chromosome, subtelomeric region / rDNA heterochromatin / rDNA heterochromatin formation / histone deacetylase / silent mating-type cassette heterochromatin formation / histone deacetylase activity / pericentric heterochromatin / heterochromatin formation / chromatin organization / chromatin / regulation of transcription by RNA polymerase II / nucleus
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
: / NITRATE ION / Histone deacetylase clr3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrugger, C. / Schalch, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_139137-1 Switzerland
CitationJournal: Mol.Cell / Year: 2016
Title: SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules.
Authors: Job, G. / Brugger, C. / Xu, T. / Lowe, B.R. / Pfister, Y. / Qu, C. / Shanker, S. / Banos Sanz, J.I. / Partridge, J.F. / Schalch, T.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase clr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,52013
Polymers73,8191
Non-polymers70212
Water3,837213
1
A: Histone deacetylase clr3
hetero molecules

A: Histone deacetylase clr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,04026
Polymers147,6372
Non-polymers1,40324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10930 Å2
ΔGint-127 kcal/mol
Surface area50970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.487, 187.259, 142.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase clr3 / Cryptic loci regulator 3


Mass: 73818.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: clr3, SPBC800.03 / Plasmid: p728 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P56523, histone deacetylase

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Non-polymers , 7 types, 225 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% Ethyleneglycol 10% PEG 8000 0.1M MOPS/HEPES 0.04M Sodium nitrate 0.04M Sodium monophosphate 0.04M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.4→46.815 Å / Num. obs: 31830 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 52.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.86
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQW (HDAC4)

2vqw


Resolution: 2.4→46.815 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.17
RfactorNum. reflection% reflection
Rfree0.2279 1524 4.79 %
Rwork0.1868 --
obs0.1888 31826 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 34 213 4952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064859
X-RAY DIFFRACTIONf_angle_d0.6466551
X-RAY DIFFRACTIONf_dihedral_angle_d11.3921757
X-RAY DIFFRACTIONf_chiral_restr0.028719
X-RAY DIFFRACTIONf_plane_restr0.003847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.3361270.27552440X-RAY DIFFRACTION90
2.4775-2.5660.27671380.25612740X-RAY DIFFRACTION100
2.566-2.66870.28141380.23822745X-RAY DIFFRACTION100
2.6687-2.79020.27961370.21932749X-RAY DIFFRACTION100
2.7902-2.93730.26061380.2142736X-RAY DIFFRACTION100
2.9373-3.12130.21651390.20212780X-RAY DIFFRACTION100
3.1213-3.36220.25541390.19242780X-RAY DIFFRACTION100
3.3622-3.70040.21141380.16692750X-RAY DIFFRACTION100
3.7004-4.23560.19411410.15762807X-RAY DIFFRACTION100
4.2356-5.33520.18651410.14172831X-RAY DIFFRACTION100
5.3352-46.82360.19491480.17162944X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4613-0.4452-0.35211.34360.07252.52690.2747-0.6336-0.02720.23560.0565-0.217-0.08720.323-0.08410.181-0.1439-0.11330.2709-0.01930.173613.024465.101-21.9546
22.2424-0.3123-0.90461.46120.25322.2357-0.02650.21660.0703-0.3122-0.055-0.34970.18110.35090.10.30430.02280.07930.23680.08020.296214.329317.9836-49.4468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 54 through 420)A54 - 420
2X-RAY DIFFRACTION2(chain 'A' and resid 421 through 680)A421 - 680

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