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- PDB-5ht2: Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex ... -

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Basic information

Entry
Database: PDB / ID: 5ht2
TitleMouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with 1-N6-etheno-adenine
Components
  • DNA
  • Tyrosyl-DNA phosphodiesterase 2
Keywordshydrolase/dna / hydrolase / dna repair / endonuclease/exonuclease/phosphatase (EEP) domain / hydrolase-dna complex
Function / homology
Function and homology information


tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / single-stranded DNA binding ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / single-stranded DNA binding / manganese ion binding / endonuclease activity / nucleolus / magnesium ion binding / cytoplasm
Similarity search - Function
: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsSchellenberg, M.J. / Vilas, C.K. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.
Authors: Schellenberg, M.J. / Perera, L. / Strom, C.N. / Waters, C.A. / Monian, B. / Appel, C.D. / Vilas, C.K. / Williams, J.G. / Ramsden, D.A. / Williams, R.S.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 26, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_poly / entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.type / _entity_src_gen.gene_src_common_name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 2
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7559
Polymers63,3384
Non-polymers4175
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-43 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.884, 68.604, 167.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein Tyrosyl-DNA phosphodiesterase 2 / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ...Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / TRAF and TNF receptor-associated protein


Mass: 28905.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: DNA chain DNA


Mass: 2763.845 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Non-polymers , 4 types, 707 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350, 200mM NaOAc, 20 mM MgOAc, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 114190 / % possible obs: 97.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.529 Å2 / Rmerge(I) obs: 0.051 / Net I/av σ(I): 20.951 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.43-1.4830.599186.6
1.48-1.543.70.379197.8
1.54-1.613.80.252199.1
1.61-1.73.90.177199.1
1.7-1.83.90.127199.1
1.8-1.943.90.09199
1.94-2.143.90.067199
2.14-2.4540.054199.7
2.45-3.084.30.049199.4
3.08-504.20.04195.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZ1

4gz1


Resolution: 1.43→29.928 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.15 10580 4.99 %
Rwork0.1161 --
obs0.1178 212129 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→29.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 25 702 5100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074738
X-RAY DIFFRACTIONf_angle_d1.186543
X-RAY DIFFRACTIONf_dihedral_angle_d15.421840
X-RAY DIFFRACTIONf_chiral_restr0.073725
X-RAY DIFFRACTIONf_plane_restr0.006782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4305-1.44670.30162660.26345113X-RAY DIFFRACTION72
1.4467-1.46370.28683120.23685618X-RAY DIFFRACTION79
1.4637-1.48160.23732800.22026126X-RAY DIFFRACTION85
1.4816-1.50030.25523330.19416531X-RAY DIFFRACTION92
1.5003-1.52010.19013410.17366858X-RAY DIFFRACTION95
1.5201-1.54090.22613670.16376853X-RAY DIFFRACTION97
1.5409-1.56290.18873710.14936914X-RAY DIFFRACTION96
1.5629-1.58620.18584170.1386856X-RAY DIFFRACTION97
1.5862-1.6110.17243420.12566861X-RAY DIFFRACTION96
1.611-1.63740.17043620.12396906X-RAY DIFFRACTION97
1.6374-1.66570.17253320.11986951X-RAY DIFFRACTION96
1.6657-1.6960.16333430.11216836X-RAY DIFFRACTION96
1.696-1.72860.13534090.10446821X-RAY DIFFRACTION96
1.7286-1.76390.13713810.10266842X-RAY DIFFRACTION96
1.7639-1.80220.16133440.10036901X-RAY DIFFRACTION96
1.8022-1.84410.13473490.09986809X-RAY DIFFRACTION96
1.8441-1.89020.14883810.09536816X-RAY DIFFRACTION95
1.8902-1.94130.14753740.09516809X-RAY DIFFRACTION96
1.9413-1.99840.1343680.08696769X-RAY DIFFRACTION95
1.9984-2.06290.12243320.08986802X-RAY DIFFRACTION96
2.0629-2.13660.11543610.09426879X-RAY DIFFRACTION96
2.1366-2.22220.13353450.09366932X-RAY DIFFRACTION97
2.2222-2.32330.14413370.09876927X-RAY DIFFRACTION97
2.3233-2.44570.14583800.10126927X-RAY DIFFRACTION97
2.4457-2.59880.14523570.10456939X-RAY DIFFRACTION97
2.5988-2.79940.14683570.10886874X-RAY DIFFRACTION97
2.7994-3.08080.15033450.11836964X-RAY DIFFRACTION97
3.0808-3.5260.13343920.11086853X-RAY DIFFRACTION97
3.526-4.44010.13443650.10666856X-RAY DIFFRACTION96
4.4401-29.93460.17323370.15836406X-RAY DIFFRACTION90

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