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- PDB-5inq: Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Ca2+ complex -

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Basic information

Entry
Database: PDB / ID: 5inq
TitleMouse Tdp2 reaction product (5'-phosphorylated DNA)-Ca2+ complex
Components
  • DNA (5'-D(P*CP*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 / manganese ion 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 / manganese ion binding / single-stranded DNA 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: 1.848 Å
AuthorsSchellenberg, M.J. / 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_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_asym_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_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_conn.ptnr2_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)63,7599
Polymers63,2424
Non-polymers5175
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-48 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.702, 67.504, 167.529
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
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*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 2715.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 362 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, 14-18% PEG3350, 200 mM sodium acetate, 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 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.848→50 Å / Num. obs: 53955 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 31.66 Å2 / Rmerge(I) obs: 0.068 / Net I/av σ(I): 21.08 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.9260.5641100
1.92-1.996.10.4091100
1.99-2.086.10.261100
2.08-2.196.10.1931100
2.19-2.336.10.151100
2.33-2.516.10.1161100
2.51-2.766.20.0861100
2.76-3.166.10.0791100
3.16-3.995.90.06199.8
3.99-505.70.048199.3

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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: 1.848→39.077 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.94
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 2745 5.1 %random
Rwork0.1575 ---
obs0.1594 53861 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.12 Å2 / Biso mean: 50.6 Å2 / Biso min: 23.9 Å2
Refinement stepCycle: final / Resolution: 1.848→39.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 368 21 374 4757
Biso mean--54.58 52.61 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014626
X-RAY DIFFRACTIONf_angle_d1.0746342
X-RAY DIFFRACTIONf_chiral_restr0.046701
X-RAY DIFFRACTIONf_plane_restr0.006748
X-RAY DIFFRACTIONf_dihedral_angle_d15.7341754
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.848-1.87990.31841290.27112410253995
1.8799-1.9140.31541370.248125032640100
1.914-1.95090.28861290.231225402669100
1.9509-1.99070.27921280.210625232651100
1.9907-2.0340.23681220.174425582680100
2.034-2.08130.23371320.176825112643100
2.0813-2.13330.21831210.174425562677100
2.1333-2.1910.23511430.169625452688100
2.191-2.25550.24471250.163525472672100
2.2555-2.32820.23091110.163325632674100
2.3282-2.41150.2111450.15825552700100
2.4115-2.5080.18981410.156825262667100
2.508-2.62210.21251580.154425492707100
2.6221-2.76030.18991500.157125292679100
2.7603-2.93320.19611450.163525632708100
2.9332-3.15960.21231280.16825822710100
3.1596-3.47740.17251500.151525912741100
3.4774-3.98010.17241540.131925892743100
3.9801-5.01290.16111510.11952614276599
5.0129-39.0860.18991460.17727622908100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30240.36530.62621.38420.22891.39970.13380.19240.0224-0.0551-0.08420.157-0.1015-0.215400.27490.00270.01070.3889-0.02380.3215-13.611-11.14094.0336
20.73940.3196-0.03660.77040.60680.55120.1580.02340.2166-0.0259-0.0557-0.0481-0.0124-0.0563-0.00010.2535-0.00790.01480.3776-0.05130.3613-6.4383-7.95325.275
31.06890.92850.59960.85410.51111.71770.0626-0.33170.40530.1565-0.042-0.1872-0.05340.00940.01130.2754-0.0299-0.01030.3872-0.10420.3875-4.64-7.214716.504
41.83351.47540.01752.67091.03481.51460.3024-0.66120.23330.375-0.1048-0.32130.1375-0.06980.11410.3776-0.0364-0.0740.5076-0.04740.2594-6.6078-18.719822.8884
51.27630.22670.73351.2508-0.33290.52420.2313-0.8781-0.20770.6321-0.0531-0.05740.3264-0.28560.03350.4659-0.1026-0.02360.6120.01820.3041-13.2124-21.393624.4142
60.72750.37140.32520.23180.18890.08820.16120.0055-0.3282-0.0289-0.12360.04590.2522-0.0824-0.00010.348-0.0354-0.01830.3578-0.03380.3618-18.007-27.09979.7301
71.87440.31750.58430.6899-0.40460.49660.0854-0.348-0.04720.1139-0.04190.07380.0538-0.234-0.00010.3384-0.05550.00430.4126-0.0510.3104-16.0994-21.808713.9721
81.51490.3390.76181.0599-0.29490.61480.02020.4255-0.09850.0129-0.16570.15650.1391-0.4421-0.00020.26730.0054-0.02520.4035-0.05370.2849-16.211-17.1274.6919
90.48240.31620.28542.44611.25980.65820.09430.22580.01350.0315-0.0095-0.6943-0.20680.34050.00250.3162-0.0373-0.02160.44360.0230.450121.1366-61.032624.713
101.0010.9983-0.52981.97290.44450.78870.02450.352-0.268-0.1535-0.1292-0.15780.0434-0.0508-0.00010.35190.03770.02020.4542-0.02380.375614.016-67.155421.0998
110.56160.44020.25550.98790.04780.55180.18760.16520.0848-0.1245-0.3398-0.23310.2395-0.18350.00050.3953-0.036-0.04740.3675-0.05930.35676.9128-72.513628.934
120.08510.1829-0.09810.83140.53880.65220.19470.2611-0.1587-0.1869-0.36820.08840.24820.0351-0.0020.40490.0131-0.0580.4574-0.04880.32531.3377-61.570923.1701
130.66870.61850.15030.54690.41830.4560.26280.0467-0.07010.1117-0.44020.01690.06730.0867-0.00650.414-0.06110.01040.35670.00640.31224.5318-62.552430.6184
141.8246-0.29840.43731.12840.62210.50570.1762-0.19160.13570.1705-0.14890.4313-0.1765-0.4355-0.00030.3943-0.00470.00070.4458-0.05080.3472-1.0783-56.25330.6296
150.39650.030.42861.5678-0.35211.38320.2748-0.12920.2530.5431-0.26220.0473-0.8099-0.06170.07920.6053-0.11020.00720.381-0.02670.32819.1567-48.517535.7388
161.71680.76970.25950.8573-0.10461.89630.2498-0.46690.30.3631-0.4032-0.136-0.32760.1048-0.04060.5267-0.098-0.05680.40890.00350.321512.0082-53.427335.0131
171.13130.16220.91062.25931.39851.14050.3126-0.24550.03380.646-0.2576-0.5532-0.14080.73260.09040.4363-0.0887-0.06880.44120.09490.430621.0167-57.315830.9959
181.72610.6819-1.37292.6582.154.29930.00141.7840.27130.1517-1.2536-0.27220.2798-0.3117-2.73450.29860.1859-0.09370.91190.32730.863410.0038-37.574312.5311
190.09170.47630.07252.8339-0.28110.08470.4952-0.31-1.26840.6698-0.41010.04250.06251.29480.83810.52560.2233-0.33940.80630.09010.82757.0371-37.80318.9101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 116 through 153 )A116 - 153
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 174 )A154 - 174
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 225 )A175 - 225
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 260 )A226 - 260
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 292 )A261 - 292
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 313 )A293 - 313
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 345 )A314 - 345
8X-RAY DIFFRACTION8chain 'A' and (resid 346 through 370 )A346 - 370
9X-RAY DIFFRACTION9chain 'B' and (resid 123 through 153 )B123 - 153
10X-RAY DIFFRACTION10chain 'B' and (resid 154 through 190 )B154 - 190
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 208 )B191 - 208
12X-RAY DIFFRACTION12chain 'B' and (resid 209 through 225 )B209 - 225
13X-RAY DIFFRACTION13chain 'B' and (resid 226 through 240 )B226 - 240
14X-RAY DIFFRACTION14chain 'B' and (resid 241 through 272 )B241 - 272
15X-RAY DIFFRACTION15chain 'B' and (resid 273 through 313 )B273 - 313
16X-RAY DIFFRACTION16chain 'B' and (resid 314 through 345 )B314 - 345
17X-RAY DIFFRACTION17chain 'B' and (resid 346 through 370 )B346 - 370
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 9 )C1 - 9
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 9 )D1 - 9

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