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- PDB-3bo5: Crystal structure of methyltransferase domain of human Histone-ly... -

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Basic information

Entry
Database: PDB / ID: 3bo5
TitleCrystal structure of methyltransferase domain of human Histone-lysine N-methyltransferase SETMAR
ComponentsHistone-lysine N-methyltransferase SETMAR
KeywordsTRANSFERASE / SET domain / methyltransferase / SETMAR / Chromatin regulator / DNA damage / DNA repair / DNA-binding / Nucleus / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / histone H3K36 dimethyltransferase activity / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing ...negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / histone H3K36 dimethyltransferase activity / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / histone H3K4 methyltransferase activity / DNA catabolic process / positive regulation of double-strand break repair via nonhomologous end joining / replication fork processing / DNA integration / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / endonuclease activity / methylation / cell population proliferation / Hydrolases; Acting on ester bonds / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Transposase, type 1 / Mos1 transposase, HTH domain / : / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like ...Transposase, type 1 / Mos1 transposase, HTH domain / : / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Ribonuclease H superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase SETMAR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsLunin, V.V. / Wu, H. / Ren, H. / Dobrovetsky, E. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Methyltransferase Domain of Human Histone-lysine N-methyltransferase SETMAR in Complex With AdoHcy.
Authors: Wu, H. / Lunin, V.V. / Ren, H. / Dobrovetsky, E. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1298
Polymers32,2991
Non-polymers8307
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.396, 67.827, 44.637
Angle α, β, γ (deg.)90.00, 105.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase SETMAR / SET domain and mariner transposase fusion gene-containing protein / Metnase / Hsmar1 [Includes: ...SET domain and mariner transposase fusion gene-containing protein / Metnase / Hsmar1 [Includes: Histone-lysine N-methyltransferase / and Mariner transposase Hsmar1]


Mass: 32298.834 Da / Num. of mol.: 1
Fragment: Histone-lysine N-methyltransferase domain: Residues 2-290
Mutation: E260A, D261S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETMAR / Plasmid: p15b / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: Q53H47, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793143, 1.2832396
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931431
21.28323961
ReflectionResolution: 1.59→42.91 Å / Num. all: 31726 / Num. obs: 31726 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.066 / Net I/σ(I): 27
Reflection shellResolution: 1.59→1.66 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3116 / Rsym value: 0.461 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.59→42.91 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.462 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.088 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19889 1606 5.1 %RANDOM
Rwork0.15516 ---
all0.15741 30096 --
obs0.15741 30096 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.33 Å2
2---0.52 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.59→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 42 304 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9833016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77423.40297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1381515
X-RAY DIFFRACTIONr_chiral_restr0.1490.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021698
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21092
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21517
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4661.51389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29422217
X-RAY DIFFRACTIONr_scbond_it2.993921
X-RAY DIFFRACTIONr_scangle_it4.4374.5793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 84 -
Rwork0.218 1880 -
obs--83.86 %

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