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- PDB-3rq4: Crystal structure of suppressor of variegation 4-20 homolog 2 -

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Basic information

Entry
Database: PDB / ID: 3rq4
TitleCrystal structure of suppressor of variegation 4-20 homolog 2
ComponentsHistone-lysine N-methyltransferase SUV420H2
KeywordsTRANSFERASE / SUV420H2 / suppressor / variegation 4-20 homolog 2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / heterochromatin => GO:0000792 / condensed chromosome, centromeric region => GO:0000779 / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / positive regulation of isotype switching / S-adenosyl-L-methionine binding / positive regulation of double-strand break repair via nonhomologous end joining / pericentric heterochromatin ...: / heterochromatin => GO:0000792 / condensed chromosome, centromeric region => GO:0000779 / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / positive regulation of isotype switching / S-adenosyl-L-methionine binding / positive regulation of double-strand break repair via nonhomologous end joining / pericentric heterochromatin / PKMTs methylate histone lysines / histone binding / DNA repair / chromatin binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Histone-lysine N-methyltransferase / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. ...Histone-lysine N-methyltransferase / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain / Beta Complex / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase KMT5C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDong, A. / Zeng, H. / Tempel, W. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2.
Authors: Wu, H. / Siarheyeva, A. / Zeng, H. / Lam, R. / Dong, A. / Wu, X.H. / Li, Y. / Schapira, M. / Vedadi, M. / Min, J.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Feb 28, 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.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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SUV420H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,64932
Polymers28,1231
Non-polymers52631
Water4,143230
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.680, 60.151, 126.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone-lysine N-methyltransferase SUV420H2 / Lysine N-methyltransferase 5C / Suppressor of variegation 4-20 homolog 2 / Su(var)4-20 homolog 2 / Suv4-20h2


Mass: 28123.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUV420H2, KMT5C, PP7130 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)V2RpRARE
References: UniProt: Q86Y97, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 261 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 28 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% PEG8K, 0.1MHepes, 12% Ethylene Glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→63.3 Å / Num. all: 25132 / Num. obs: 25132 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 26.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.55 / Num. unique all: 1050 / Rsym value: 0.358 / % possible all: 83.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
Coot0.6model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUV420H1

Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.163 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22115 805 3.2 %RANDOM
Rwork0.17834 ---
all0.17975 25132 --
obs0.17975 24269 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.37 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 60 230 2162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222029
X-RAY DIFFRACTIONr_bond_other_d0.0010.021412
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9742765
X-RAY DIFFRACTIONr_angle_other_deg0.90333416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.73722.6694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65915332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6991520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02444
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7771.51250
X-RAY DIFFRACTIONr_mcbond_other0.2241.5505
X-RAY DIFFRACTIONr_mcangle_it1.3722012
X-RAY DIFFRACTIONr_scbond_it2.2543779
X-RAY DIFFRACTIONr_scangle_it3.6354.5745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 43 -
Rwork0.277 1529 -
obs--85.81 %
Refinement TLS params.Method: refined / Origin x: 20.2704 Å / Origin y: 18.0271 Å / Origin z: 81.021 Å
111213212223313233
T0.0175 Å20 Å2-0.0005 Å2-0.0553 Å2-0.0098 Å2--0.0359 Å2
L1.2324 °20.2446 °2-0.1185 °2-1.94 °2-0.5682 °2--1.5844 °2
S0.0168 Å °0.0133 Å °-0.0328 Å °-0.0463 Å °0.0005 Å °-0.0758 Å °0.1368 Å °-0.0034 Å °-0.0173 Å °

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