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- PDB-5ikj: Structure of Clr2 bound to the Clr1 C-terminus -

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Basic information

Entry
Database: PDB / ID: 5ikj
TitleStructure of Clr2 bound to the Clr1 C-terminus
Components
  • Cryptic loci regulator 2
  • Cryptic loci regulator protein 1
KeywordsTRANSCRIPTION / Methyl-CpG-binding domain / BAH domain / chromobarrel domain / complex / Cell cycle
Function / homology
Function and homology information


SHREC complex / : / CENP-A containing chromatin / : / mating-type region heterochromatin / heterochromatin formation => GO:0031507 / chromosome, subtelomeric region / rDNA heterochromatin / silent mating-type cassette heterochromatin formation / pericentric heterochromatin ...SHREC complex / : / CENP-A containing chromatin / : / mating-type region heterochromatin / heterochromatin formation => GO:0031507 / chromosome, subtelomeric region / rDNA heterochromatin / silent mating-type cassette heterochromatin formation / pericentric heterochromatin / heterochromatin formation / chromatin organization / nucleus / metal ion binding
Similarity search - Function
Cryptic loci regulator 2, C-terminal / Cryptic loci regulator 2, N-terminal / Cryptic loci regulator 2 / Transcription-silencing protein Clr2 / Transcription-silencing protein, cryptic loci regulator Clr2 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Cryptic loci regulator 2 / Cryptic loci regulator protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPfister, Y. / 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptic loci regulator 2
B: Cryptic loci regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9755
Polymers72,8392
Non-polymers1363
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-62 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.499, 103.499, 135.090
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 Cryptic loci regulator 2


Mass: 63119.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: T7-tagged Clr2 full length
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: clr2, SPAC1B3.17 / Plasmid: p724 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O13881
#2: Protein Cryptic loci regulator protein 1


Mass: 9719.022 Da / Num. of mol.: 1 / Fragment: UNP residues 1151-1238
Source method: isolated from a genetically manipulated source
Details: Clr1 residues 1151-1238
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: clr1, SPBC2D10.17 / Plasmid: p724 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O74808
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M Tris-bicine 30 mM Sodium Fluoride 30 mM Sodium Bromide 30 mM Sodium Iodide 18% Ethylene glycol 9% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763,0.9792,0.9763,0.9792
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97921
ReflectionResolution: 2.3→48.325 Å / Num. obs: 37719 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 54.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→48.325 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 3588 5 %
Rwork0.2137 --
obs0.2152 37690 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 3 70 4262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024506
X-RAY DIFFRACTIONf_angle_d0.5236103
X-RAY DIFFRACTIONf_dihedral_angle_d13.7922681
X-RAY DIFFRACTIONf_chiral_restr0.041653
X-RAY DIFFRACTIONf_plane_restr0.002784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33030.3341590.33112610X-RAY DIFFRACTION100
2.3303-2.36220.33151210.31432647X-RAY DIFFRACTION100
2.3622-2.3960.30651260.28952600X-RAY DIFFRACTION100
2.396-2.43170.3491350.29752633X-RAY DIFFRACTION100
2.4317-2.46970.34831430.28352637X-RAY DIFFRACTION100
2.4697-2.51020.29441350.28432565X-RAY DIFFRACTION100
2.5102-2.55350.35531290.28152657X-RAY DIFFRACTION100
2.5535-2.59990.37121410.27062649X-RAY DIFFRACTION100
2.5999-2.64990.31831330.27092617X-RAY DIFFRACTION100
2.6499-2.7040.30571320.26882676X-RAY DIFFRACTION100
2.704-2.76280.32371380.26592554X-RAY DIFFRACTION100
2.7628-2.82710.30361230.25082666X-RAY DIFFRACTION100
2.8271-2.89770.27371240.25562641X-RAY DIFFRACTION100
2.8977-2.97610.30371430.24772604X-RAY DIFFRACTION100
2.9761-3.06360.30641270.252645X-RAY DIFFRACTION100
3.0636-3.16250.27991590.23272615X-RAY DIFFRACTION100
3.1625-3.27550.25961390.23912629X-RAY DIFFRACTION100
3.2755-3.40660.28081640.22172593X-RAY DIFFRACTION100
3.4066-3.56160.25891360.21462656X-RAY DIFFRACTION100
3.5616-3.74930.22441280.20312589X-RAY DIFFRACTION100
3.7493-3.98410.2281290.20522689X-RAY DIFFRACTION100
3.9841-4.29160.21941860.17732550X-RAY DIFFRACTION100
4.2916-4.72310.17181440.17162623X-RAY DIFFRACTION100
4.7231-5.40580.22891430.17182620X-RAY DIFFRACTION100
5.4058-6.80770.22141120.20722655X-RAY DIFFRACTION100
6.8077-48.33570.19111390.19392609X-RAY DIFFRACTION99

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