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- PDB-5ino: Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex -

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Basic information

Entry
Database: PDB / ID: 5ino
TitleHuman Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ 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 / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Nonhomologous End-Joining (NHEJ) / PML body / transcription corepressor activity / double-strand break repair ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Nonhomologous End-Joining (NHEJ) / PML body / transcription corepressor activity / double-strand break repair / single-stranded DNA binding / manganese ion binding / cell surface receptor signaling pathway / nuclear body / nucleolus / magnesium ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
UBA-like domain / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.205 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 ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1915
Polymers64,0954
Non-polymers961
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-35 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.663, 69.663, 120.677
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Tyrosyl-DNA phosphodiesterase 2 / hTDP2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ETS1-associated protein 2 ...hTDP2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ETS1-associated protein 2 / ETS1-associated protein II / EAPII / TRAF and TNF receptor-associated protein / Tyrosyl-RNA phosphodiesterase / VPg unlinkase


Mass: 29331.805 Da / Num. of mol.: 2 / Fragment: unp residues 138-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP2, EAP2, TTRAP, AD-022 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O95551, 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)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 27% PEG600, 90 mM TRIS, 9% glycerol, 450 mM ammonium sulfate

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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: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 10786 / % possible obs: 100 % / Redundancy: 3.9 % / Biso Wilson estimate: 97.03 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.001 / Net I/av σ(I): 15.548 / Net I/σ(I): 8.5 / Num. measured all: 41889
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.2-3.313.90.5741100
3.31-3.453.90.3821100
3.45-3.63.90.2791100
3.6-3.793.90.2121100
3.79-4.033.90.1531100
4.03-4.343.90.1091100
4.34-4.783.90.0821100
4.78-5.473.90.0671100
5.47-6.893.90.0671100
6.89-503.70.043199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4gz1


Resolution: 3.205→34.832 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 518 4.82 %random
Rwork0.2136 ---
obs0.216 10757 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 383.9 Å2 / Biso mean: 147.88 Å2 / Biso min: 61.79 Å2
Refinement stepCycle: final / Resolution: 3.205→34.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 368 5 5 4373
Biso mean--225.84 83.32 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034491
X-RAY DIFFRACTIONf_angle_d0.7836145
X-RAY DIFFRACTIONf_chiral_restr0.049682
X-RAY DIFFRACTIONf_plane_restr0.003720
X-RAY DIFFRACTIONf_dihedral_angle_d16.6511703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2054-3.52770.30761370.284125602697
3.5277-4.03750.32521190.249725492668
4.0375-5.08430.26841240.207525812705
5.0843-34.83350.23071380.186525492687
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)
15.24585.5080.83866.7752-2.01777.9221-1.2282-1.4265-0.04082.5519-0.2759-0.82610.56120.510.69051.0210.07660.05040.98780.07680.425415.2834-14.9396-3.1221
27.18972.00293.26295.51034.83614.62340.659-2.1204-1.57182.4165-1.39480.8809-0.580.21761.16171.71560.24290.30662.31210.20071.125515.5654-19.58054.7259
37.7573-1.80533.63577.384-1.41957.8451-0.6387-1.3202-2.0996-0.4744-0.56730.85191.2205-1.4407-0.82711.09370.3290.23840.88810.36910.68911.3092-24.1122-5.9381
43.92352.91533.29876.78010.1784.8574-1.1113-0.338-0.488-0.99790.18350.2087-0.9804-0.43720.41751.1510.30510.03160.6475-0.05470.833210.812-20.1658-16.7343
53.69545.3105-0.55367.91011.10979.0027-0.3999-0.9419-0.0666-1.44470.34970.09-0.6454-0.26820.23050.99030.0640.33480.35470.06310.737919.1967-17.2376-17.0938
64.54721.6810.93997.64451.75222.2866-1.35891.7858-0.4929-1.66560.5434-0.2689-1.29470.44520.55091.4348-0.13150.1190.91660.01430.684819.8719-14.6026-23.3677
76.3617-3.93220.96175.4518-4.09719.6414-0.78261.57891.2018-0.80220.1594-1.342-1.8081.67440.49921.5202-0.53620.15630.8627-0.00180.980229.1606-10.1781-20.649
89.16077.1675-1.22246.66691.94667.5167-0.3571-1.52340.015-0.6041-0.2807-0.9827-1.41021.71440.68871.18920.03770.08581.3349-0.00170.806129.2132-10.8021-6.9081
93.64224.2224-1.85976.45940.26234.43270.4074-2.0049-0.59480.6941-0.1410.1988-0.74040.111-0.00380.7698-0.0126-0.01061.190.04860.388618.7534-8.919-4.2604
104.3296-2.5845-4.11576.31767.08559.9624-0.7847-0.2679-0.61611.0729-1.61741.788-1.62470.21670.86271.1428-0.09710.00471.2040.48011.938841.8095-35.0678-12.3718
115.9672-3.1789-3.55342.69684.36648.753-0.14440.0273-3.18440.940.32491.78832.1058-0.45160.3470.54040.37910.02821.59040.79382.831841.3424-32.8248-9.6991
124.0291-1.2563.73524.01642.80537.8528-0.3662-0.0386-0.9004-1.38340.67050.66272.2604-0.92280.59131.32910.00610.05720.37280.17690.946367.4937-43.5543-25.6448
139.08270.9165-6.92013.44461.38166.5764-0.5199-1.3301-1.76160.4405-0.1966-0.37092.48821.11090.21571.70310.090.06730.59620.37291.396169.6939-50.9946-22.6377
146.794-0.2019-0.82167.0290.51383.7354-0.29-0.6462-0.8962-2.0517-0.1422-0.03290.59170.71380.30041.34640.13230.19480.6290.15290.893273.0761-42.4601-20.4798
158.1951-3.4836-5.01553.90262.48537.0133-0.1875-0.83090.839-0.1630.1452-0.5226-0.3722-0.2298-0.42881.42890.0530.30990.7019-0.0660.933874.2681-36.4374-18.5121
169.05470.46261.40485.88214.737.58930.45650.9229-0.5045-1.2138-0.3317-0.5066-0.25270.20870.0331.57760.02790.19920.7843-0.11680.709379.3664-32.8562-27.1773
178.2374-3.296-2.34645.04165.45636.18320.624-0.73741.5966-1.98660.57560.2027-1.12520.5506-0.91461.3848-0.0915-0.00090.6896-0.03590.755468.2223-26.9006-23.1076
187.45196.46840.69926.21110.35880.1495-1.24121.3698-0.3711-1.80041.5534-0.87210.2104-0.40163.5181.5801-0.0572-0.58150.7180.73690.665169.3626-30.5106-29.655
198.99193.1187-3.58291.0517-1.22795.2754-0.18880.69482.5756-0.95220.6451.4861-1.792-1.0811-1.16991.73880.2735-0.46760.7610.33921.471559.2113-23.1553-28.1924
206.9060.2267-2.65984.78294.07554.93960.17041.94852.7484-2.60870.74551.6577-0.3764-0.9921-0.5751.7051-0.2207-0.59380.91090.37071.215160.8449-28.3675-33.8941
217.8243-7.59844.0569.187-4.94862.69670.56160.7217-2.0897-2.05171.5242.10111.0168-1.1465-0.86192.1374-0.4118-0.0461.4505-0.0450.887160.5222-32.6953-42.4194
225.86210.8517-4.48218.952-3.86994.58270.13070.4526-1.8706-0.8794-0.09431.53910.518-2.31350.20841.2211-0.2374-0.41711.32210.28531.681551.983-44.886-28.9081
234.84180.17225.00497.69-4.81248.05320.13640.2144-0.2175-1.17660.56020.82050.70720.4457-0.43921.7665-0.14840.04840.993-0.04770.759866.7656-41.0194-36.1379
247.69075.253-4.55978.3711-7.78377.4217-0.5769-0.0225-2.8756-2.78440.31520.65531.84070.1669-0.0151.407-0.5525-0.39710.8540.19921.29664.7852-45.0096-31.235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 108 through 128 )A108 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 143 )A129 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 180 )A144 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 215 )A181 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 233 )A216 - 233
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 262 )A234 - 262
7X-RAY DIFFRACTION7chain 'A' and (resid 263 through 282 )A263 - 282
8X-RAY DIFFRACTION8chain 'A' and (resid 283 through 321 )A283 - 321
9X-RAY DIFFRACTION9chain 'A' and (resid 322 through 361 )A322 - 361
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 9 )C1 - 9
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 9 )D1 - 9
12X-RAY DIFFRACTION12chain 'B' and (resid 111 through 128 )B111 - 128
13X-RAY DIFFRACTION13chain 'B' and (resid 129 through 143 )B129 - 143
14X-RAY DIFFRACTION14chain 'B' and (resid 144 through 164 )B144 - 164
15X-RAY DIFFRACTION15chain 'B' and (resid 165 through 180 )B165 - 180
16X-RAY DIFFRACTION16chain 'B' and (resid 181 through 198 )B181 - 198
17X-RAY DIFFRACTION17chain 'B' and (resid 199 through 215 )B199 - 215
18X-RAY DIFFRACTION18chain 'B' and (resid 216 through 230 )B216 - 230
19X-RAY DIFFRACTION19chain 'B' and (resid 231 through 250 )B231 - 250
20X-RAY DIFFRACTION20chain 'B' and (resid 251 through 273 )B251 - 273
21X-RAY DIFFRACTION21chain 'B' and (resid 274 through 291 )B274 - 291
22X-RAY DIFFRACTION22chain 'B' and (resid 292 through 315 )B292 - 315
23X-RAY DIFFRACTION23chain 'B' and (resid 316 through 345 )B316 - 345
24X-RAY DIFFRACTION24chain 'B' and (resid 346 through 360 )B346 - 360

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