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- PDB-3f2k: Structure of the transposase domain of human Histone-lysine N-met... -

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Basic information

Entry
Database: PDB / ID: 3f2k
TitleStructure of the transposase domain of human Histone-lysine N-methyltransferase SETMAR
Components
  • Histone-lysine N-methyltransferase SETMAR
  • LYFA Peptide
KeywordsTRANSFERASE / Histone-lysine N-methyltransferase SETMAR / SET domain and mariner transposase fusion / SET domain and mariner transposase fusion gene-containing protein / Structural Genomics / Structural Genomics Consortium / SGC / Alternative splicing / Chromatin regulator / Coiled coil / DNA damage / DNA repair / DNA-binding / Methyltransferase / Nucleus / Phosphoprotein
Function / homology
Function and homology information


negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / histone H3K36 dimethyltransferase 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 / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / histone H3K36 dimethyltransferase activity / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / DNA catabolic process / histone H3K4 methyltransferase activity / 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 / Hydrolases; Acting on ester bonds / cell population proliferation / 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 / Post-SET domain ...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 / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETMAR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAmaya, M.F. / Dombrovski, L. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. ...Amaya, M.F. / Dombrovski, L. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Transposase Domain of Human Histone-lysine N-methyltransferase SETMAR.
Authors: Dombrovski, L. / Amaya, M.F. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETMAR
B: Histone-lysine N-methyltransferase SETMAR
C: LYFA Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1135
Polymers54,0643
Non-polymers492
Water7,314406
1
A: Histone-lysine N-methyltransferase SETMAR
C: LYFA Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3133
Polymers27,2882
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-5 kcal/mol
Surface area10520 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase SETMAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8002
Polymers26,7761
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.826, 46.521, 61.748
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-271-

HOH

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Components

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


Mass: 26775.861 Da / Num. of mol.: 2 / Fragment: transposase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETMAR / Production host: Escherichia coli (E. coli)
References: UniProt: Q53H47, histone-lysine N-methyltransferase
#2: Protein/peptide LYFA Peptide


Mass: 512.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Purified SETMAR transposase domain was crystallized in 20% PEG 3350, 0.2 M di-Na Tartrate., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.504 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.504 Å / Relative weight: 1
ReflectionHighest resolution: 1.85 Å / Num. all: 36815 / Num. obs: 36815

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F7T

2f7t


Resolution: 1.85→79.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.112 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25617 1846 5 %RANDOM
Rwork0.20494 ---
obs0.20764 34969 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.49 Å2
2--0.24 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.85→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 2 406 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9294380
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09124.793169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70915505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3071514
X-RAY DIFFRACTIONr_chiral_restr0.1290.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022522
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21676
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2326
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2541.52015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85323141
X-RAY DIFFRACTIONr_scbond_it2.90731388
X-RAY DIFFRACTIONr_scangle_it4.0564.51236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 147 -
Rwork0.254 2593 -
obs--97.09 %

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