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

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Basic information

Entry
Database: PDB / ID: 5inl
TitleMouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with deoxyadenosine
Components
  • DNA (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3')
  • Tyrosyl-DNA phosphodiesterase 2
Keywordshydrolase/dna / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 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
DepositionMar 7, 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 1.4Sep 27, 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
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_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_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.pdbx_dist_value / _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

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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 (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3')
D: DNA (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7079
Polymers63,2904
Non-polymers4175
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-46 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.903, 69.051, 167.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Fragment: unp residues 118-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / 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 (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 2739.824 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 705 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.: 700 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 14% PEG3350, 100mM HEPES, 200mM NaOAc, 25 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 91961 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 19.51 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.031 / Rrim(I) all: 0.074 / Χ2: 1.003 / Net I/av σ(I): 19.378 / Net I/σ(I): 13.7 / Num. measured all: 495891
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.55-1.613.70.588191.5
1.61-1.6750.423199.1
1.67-1.755.60.3071100
1.75-1.845.60.2061100
1.84-1.955.70.1411100
1.95-2.15.70.1041100
2.1-2.325.70.0861100
2.32-2.655.70.071100
2.65-3.345.70.0651100
3.34-505.40.047199.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZ1

4gz1


Resolution: 1.551→34.078 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.34
RfactorNum. reflection% reflectionSelection details
Rfree0.1681 4604 5.01 %random
Rwork0.1292 ---
obs0.1312 91871 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.15 Å2 / Biso mean: 29.1667 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 1.551→34.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 372 25 721 5115
Biso mean--53.02 46.29 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054786
X-RAY DIFFRACTIONf_angle_d0.8486600
X-RAY DIFFRACTIONf_chiral_restr0.054736
X-RAY DIFFRACTIONf_plane_restr0.006791
X-RAY DIFFRACTIONf_dihedral_angle_d17.0261867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5513-1.56890.26771290.21992292242178
1.5689-1.58740.23291520.19862597274992
1.5874-1.60670.2111590.16852767292694
1.6067-1.62710.22061220.1572793291597
1.6271-1.64850.17621620.147229283090100
1.6485-1.6710.20991310.143729283059100
1.671-1.69490.19411540.134729223076100
1.6949-1.72020.19231620.118128823044100
1.7202-1.74710.16851600.105929253085100
1.7471-1.77570.13721590.104329353094100
1.7757-1.80640.17121440.099929203064100
1.8064-1.83920.14511450.100629553100100
1.8392-1.87460.15031690.099829093078100
1.8746-1.91280.15931500.108429133063100
1.9128-1.95440.16831680.115329163084100
1.9544-1.99990.16791560.10329173073100
1.9999-2.04990.15131480.102529573105100
2.0499-2.10530.15221460.106829403086100
2.1053-2.16720.13811500.107729293079100
2.1672-2.23720.16821510.110429723123100
2.2372-2.31710.17171510.117129513102100
2.3171-2.40990.18531500.120529503100100
2.4099-2.51950.17041580.125929683126100
2.5195-2.65230.15081570.126729463103100
2.6523-2.81840.19551560.132329693125100
2.8184-3.03590.17911480.143630113159100
3.0359-3.34120.1671800.133429533133100
3.3412-3.82410.16941660.125230143180100
3.8241-4.81580.13621460.123930603206100
4.8158-34.08620.18381750.17523148332398

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