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- PDB-1mvx: structure of the SET domain histone lysine methyltransferase Clr4 -

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Basic information

Entry
Database: PDB / ID: 1mvx
Titlestructure of the SET domain histone lysine methyltransferase Clr4
ComponentsCRYPTIC LOCI REGULATOR 4
KeywordsTRANSFERASE / lysine methyltransferase / clr4 / set-domain
Function / homology
Function and homology information


CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase ...CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / ubiquitin-modified histone reader activity / chromosome, subtelomeric region / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / pericentric heterochromatin formation / protein-lysine N-methyltransferase activity / spindle pole body / silent mating-type cassette heterochromatin formation / histone methyltransferase activity / pericentric heterochromatin / histone reader activity / ubiquitin binding / methyltransferase activity / single-stranded DNA binding / methylation / double-stranded DNA binding / single-stranded RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Histone-lysine N-methyltransferase, H3 lysine-9 specific
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMin, J.R. / Zhang, X. / Cheng, X.D. / Grewal, S.I.S. / Xu, R.-M.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the SET domain histone lysine methyltransferase Clr4.
Authors: Min, J. / Zhang, X. / Cheng, X. / Grewal, S.I. / Xu, R.M.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRYPTIC LOCI REGULATOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2756
Polymers33,9241
Non-polymers3515
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.460, 75.460, 189.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-504-

NI

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Components

#1: Protein CRYPTIC LOCI REGULATOR 4 / lysine methyltransferase CLR4


Mass: 33923.895 Da / Num. of mol.: 1 / Fragment: Residues 192-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: O60016
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: ammonium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
25 mMTris1droppH8.0
3200 mM1dropNaCl
41 mMdithiothreitol1drop
50.7-1.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 6530 / Num. obs: 6530 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 237473 / Rmerge(I) obs: 0.123

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2863 560 RANDOM
Rwork0.2159 --
all-6528 -
obs-6524 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.842 Å2-6.896 Å20 Å2
2---7.842 Å20 Å2
3---15.683 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 9 51 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it3.1671.5
X-RAY DIFFRACTIONo_mcangle_it5.2352
X-RAY DIFFRACTIONo_scbond_it4.5862
X-RAY DIFFRACTIONo_scangle_it6.782.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Rfactor Rfree: 0.283 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.43
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg24.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg1.03

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