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- PDB-3k9j: Transposase domain of Metnase -

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Basic information

Entry
Database: PDB / ID: 3k9j
TitleTransposase domain of Metnase
ComponentsHistone-lysine N-methyltransferase SETMAR
KeywordsTRANSFERASE / transposase / Chromatin regulator / 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 / histone H3K36 dimethyltransferase activity / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA double-strand break processing / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity ...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 / DNA double-strand break processing / nucleic acid metabolic process / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / DNA catabolic process / replication fork processing / positive regulation of double-strand break repair via nonhomologous end joining / double-strand break repair via nonhomologous end joining / DNA integration / single-stranded DNA binding / site of double-strand break / methylation / double-stranded DNA binding / endonuclease activity / 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 domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Post-SET domain / Post-SET domain profile. ...Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Pre-SET domain / Pre-SET motif / 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 superfamily / SET domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsGoodwin, K.D. / He, H. / Imasaki, T. / Lee, S.-H. / Georgiadis, M.M.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structure of the human Hsmar1-derived transposase domain in the DNA repair enzyme Metnase.
Authors: Goodwin, K.D. / He, H. / Imasaki, T. / Lee, S.H. / Georgiadis, M.M.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4218
Polymers57,0712
Non-polymers3506
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone-lysine N-methyltransferase SETMAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8246
Polymers28,5351
Non-polymers2885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Histone-lysine N-methyltransferase SETMAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5972
Polymers28,5351
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.158, 45.411, 90.678
Angle α, β, γ (deg.)90.00, 113.81, 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 / Histone- ...SET domain and mariner transposase fusion gene-containing protein / Metnase / Hsmar1 / Histone-lysine N-methyltransferase / Mariner transposase Hsmar1


Mass: 28535.418 Da / Num. of mol.: 2 / Mutation: N566R, G569R, A649W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETMAR / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: Q53H47, histone-lysine N-methyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE DNA USED FOR THE STUDIES ENCODES A GLU FOR POSITION 438, WHICH MIGHT BE A ...AUTHORS STATE THAT THE DNA USED FOR THE STUDIES ENCODES A GLU FOR POSITION 438, WHICH MIGHT BE A NATURAL VARIANT.

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: NH4OAc, CaCl2, PEG4000, pH 8.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.10546 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10546 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 43992 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.046 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.9-1.933.20.42571.1
1.93-1.973.30.34778.4
1.97-2.013.40.35381.7
2.01-2.053.60.28185.3
2.05-2.093.70.25988.6
2.09-2.143.70.23392
2.14-2.193.80.21995.4
2.19-2.253.90.19997.9
2.25-2.3240.17698.7
2.32-2.394.10.15599.5
2.39-2.484.10.13699.8
2.48-2.584.20.113100
2.58-2.74.20.096100
2.7-2.844.20.084100
2.84-3.024.20.075100
3.02-3.254.20.064100
3.25-3.584.20.049100
3.58-4.094.20.039100
4.09-5.164.10.03299.7
5.16-503.90.03395.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_4refinement
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→44.585 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: -0 / σ(F): 0.04 / Phase error: 25.04 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.234 2047 4.95 %
Rwork0.2047 --
obs0.2061 41365 88.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.646 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2229 Å2-0 Å212.4407 Å2
2---6.3261 Å2-0 Å2
3---2.1032 Å2
Refinement stepCycle: LAST / Resolution: 1.903→44.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 21 251 3661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073506
X-RAY DIFFRACTIONf_angle_d1.0524748
X-RAY DIFFRACTIONf_dihedral_angle_d18.8681286
X-RAY DIFFRACTIONf_chiral_restr0.078497
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.903-1.94680.27870.25871714X-RAY DIFFRACTION58
1.9468-1.99550.26921200.24711986X-RAY DIFFRACTION69
1.9955-2.04950.25651240.22812159X-RAY DIFFRACTION74
2.0495-2.10980.26661400.22572354X-RAY DIFFRACTION80
2.1098-2.17790.2461300.21172489X-RAY DIFFRACTION85
2.1779-2.25570.25331130.20672668X-RAY DIFFRACTION89
2.2557-2.3460.26071390.21182687X-RAY DIFFRACTION92
2.346-2.45280.25671370.20762791X-RAY DIFFRACTION94
2.4528-2.58210.23841440.20272805X-RAY DIFFRACTION95
2.5821-2.74380.23171300.19832904X-RAY DIFFRACTION97
2.7438-2.95560.27131480.21482892X-RAY DIFFRACTION98
2.9556-3.2530.25211700.2192945X-RAY DIFFRACTION99
3.253-3.72350.21671490.192949X-RAY DIFFRACTION100
3.7235-4.69040.19411440.16992999X-RAY DIFFRACTION99
4.6904-44.59690.21361720.21392976X-RAY DIFFRACTION97
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

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