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- PDB-5inn: Mouse Tdp2 D358N protein, apo state with increased disorder among... -

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Basic information

Entry
Database: PDB / ID: 5inn
TitleMouse Tdp2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp conformations
ComponentsTyrosyl-DNA phosphodiesterase 2
KeywordsHYDROLASE / dna repair / endonuclease/exonuclease/phosphatase (EEP) domain
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
Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchellenberg, M.J. / Appel, C.D. / 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 / Structure summary
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
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
B: Tyrosyl-DNA phosphodiesterase 2
C: Tyrosyl-DNA phosphodiesterase 2
D: Tyrosyl-DNA phosphodiesterase 2
E: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,06812
Polymers144,5215
Non-polymers5477
Water2,666148
1
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0923
Polymers28,9041
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9402
Polymers28,9041
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0363
Polymers28,9041
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0002
Polymers28,9041
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0002
Polymers28,9041
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.440, 114.880, 115.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: 28904.246 Da / Num. of mol.: 5 / Fragment: unp residues 118-370 / Mutation: D358N
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14-18% PEG3350, 100mM HEPES, 200mM lithium sulfate, 10mM 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: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30546 / % possible obs: 95.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 45.96 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.061 / Rrim(I) all: 0.129 / Χ2: 0.971 / Net I/av σ(I): 10.556 / Net I/σ(I): 6.2 / Num. measured all: 127542
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.93.40.459193
2.9-3.0240.379197.8
3.02-3.154.30.277197.9
3.15-3.324.30.192197.7
3.32-3.534.30.14197.3
3.53-3.84.30.108196.9
3.8-4.184.30.083196.2
4.18-4.794.30.07195.4
4.79-6.034.30.079194.1
6.03-504.20.052190.8

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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: 2.8→49.393 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.19
RfactorNum. reflection% reflection
Rfree0.2555 1543 5.17 %
Rwork0.2128 --
obs0.2151 29851 49.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.71 Å2 / Biso mean: 52.9844 Å2 / Biso min: 5.68 Å2
Refinement stepCycle: final / Resolution: 2.8→49.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9386 0 28 148 9562
Biso mean--83.97 28.33 -
Num. residues----1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029647
X-RAY DIFFRACTIONf_angle_d0.57713045
X-RAY DIFFRACTIONf_chiral_restr0.0271444
X-RAY DIFFRACTIONf_plane_restr0.0021661
X-RAY DIFFRACTIONf_dihedral_angle_d9.9283555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8003-2.89070.34631160.30231960207638
2.8907-2.9940.3761260.28172500262648
2.994-3.11390.31251400.26972657279751
3.1139-3.25560.27461420.24322657279951
3.2556-3.42720.29311270.24052672279951
3.4272-3.64180.27521430.21582650279351
3.6418-3.92290.25171470.19412635278251
3.9229-4.31750.23031360.18522642277851
4.3175-4.94170.18461440.1562642278651
4.9417-6.22410.23191570.20322616277351
6.2241-49.40090.25861650.22182677284252
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)
16.1011-0.82480.45116.25990.37384.440.22090.0657-0.0384-0.4988-0.1842-0.5022-0.17180.4804-0.01040.2423-0.07280.00190.27230.04810.267657.5698-29.8425-3.7974
23.45760.12950.85588.1267-0.44384.0470.0887-0.26050.04290.5059-0.08390.0677-0.12990.1621-0.01990.1606-0.0378-0.02250.28970.0280.220449.7396-32.85336.9987
38.84721.02490.68455.1888-2.29196.75070.0892-0.0801-0.53290.30510.31550.35820.5451-0.3308-0.25030.247-0.0635-0.07830.24580.06430.365141.317-43.66124.685
46.9705-0.47991.19554.7757-2.75764.86130.17260.8771-0.6625-0.98820.09540.1941.1566-0.0037-0.29360.5781-0.0207-0.22850.3692-0.04870.475744.4572-43.2247-9.2717
52.37720.467-1.6144.2399-1.04477.48890.2238-0.34880.4056-0.08880.55050.5686-0.2307-0.9697-0.57530.3765-0.0697-0.17030.43560.14250.432937.1829-33.7083-4.9109
68.3506-1.48430.00085.3108-0.84893.69-0.10541.3754-0.7084-1.0101-0.2358-0.05990.33390.07660.1960.4653-0.0650.06240.2996-0.05740.322553.6878-33.8176-11.202
76.00890.62910.08266.5233-1.09294.58440.0683-0.72770.1260.6317-0.1106-0.3522-0.15260.2467-0.00650.25330.0146-0.03540.2712-0.04780.218259.2921-6.167-18.3635
83.41560.76940.20114.40880.60344.2004-0.00940.1136-0.0104-0.38760.00610.2220.31960.12440.04130.1920.03850.0110.26630.03940.188348.8925-14.0093-29.8165
94.53861.7823-1.83246.0540.63847.1395-0.10760.6912-0.829-0.8948-0.639-0.72151.47371.02490.48140.44380.0240.1480.4460.05910.303258.468-17.8876-32.5636
107.1304-0.3321.19075.7435-1.62626.7667-0.02520.1868-0.1358-0.041-0.3143-0.3983-0.10921.05280.43220.2416-0.0263-0.00310.252-0.00840.385365.492-9.9342-28.7698
114.83882.19881.94316.66551.79096.00090.3083-0.3662-0.42081.0801-0.2798-0.2282-0.19870.1925-0.94620.5494-0.20470.1621-0.0243-0.31060.419422.6219-0.8662-7.4674
125.60391.944-0.78434.7504-0.35612.58040.0761-0.258-0.29190.1884-0.0219-0.19930.07170.0562-0.04070.23210.00970.05010.2219-0.00290.320329.2432-4.3285-11.6974
136.97921.8647-0.09134.8759-0.00562.17010.04520.2291.2847-0.1538-0.01040.2891-0.2391-0.3305-0.00750.23470.03270.050.36780.06850.486922.48689.5435-21.1644
147.07290.2041.96256.82250.90833.3017-0.23990.01030.31240.68360.24070.25050.1620.37670.01330.26030.04620.10890.28740.05130.550815.96840.0047-14.3501
155.72380.24752.53886.2119-0.78431.6854-0.257-0.7573-0.98361.1191-0.51590.72480.14340.25130.64320.3873-0.16540.03890.33060.12670.40839.253821.81383.0137
162.9192-0.09260.6474.8407-0.4830.1821-0.4204-0.3677-0.26580.99270.14390.32331.0212-0.46430.27680.6377-0.2080.17220.4333-0.07170.392536.717517.69513.9606
171.2659-3.3515-2.91099.37477.3087.0549-0.7383-0.6333-1.11831.3262-0.49581.64271.6976-0.3431.08151.0531-0.02220.26750.53040.0910.759838.917113.176411.1717
183.8306-0.6333-2.26994.02981.38624.2044-0.202-0.97280.09060.67610.6531-0.54450.79220.7207-0.30720.54460.2295-0.13920.6121-0.0430.342850.919422.38279.2138
191.88091.6198-0.4163.1789-2.39392.4571-0.176-0.7610.45410.62150.3686-1.1582-0.11261.2011-0.09420.3360.0779-0.10780.7605-0.25060.543257.653528.61473.6236
209.4747-6.5517-6.39187.2475.28568.49260.99370.11181.3665-0.6103-0.0496-1.584-1.19031.0935-0.8520.5233-0.1667-0.02560.699-0.14550.695454.112236.1434-3.1574
215.37732.5429-0.76527.0190.92968.09560.13820.11840.408-0.06280.03060.3271-0.39980.101-0.12120.3043-0.0068-0.04530.2844-0.02670.271446.018827.9372-7.6713
225.18352.409-0.33712.0799-0.27323.51580.19540.77450.19840.3029-0.72760.83870.2602-1.38150.63690.441-0.1230.02990.5527-0.23630.495235.704622.6002-2.6282
230.7525-0.94-1.25354.8573-1.57864.9920.1032-0.9955-0.48480.36-0.1212-0.77560.07170.1754-0.07270.3411-0.0231-0.12810.50290.09040.362864.786-16.195437.5783
244.80410.5580.53947.2668-0.40353.9686-0.0930.3961-0.0399-0.37810.0817-0.370.44440.14530.05240.3045-0.01610.01390.2844-0.01170.210764.4398-11.810722.5818
255.02630.52361.15526.5771.89647.1763-0.61040.27841.0647-0.70840.39080.3913-0.5669-0.57220.20890.2491-0.0177-0.09830.37560.02090.475454.6283-3.74920.8162
261.96230.84050.31923.48950.76520.82580.0146-0.9980.4653-0.09910.20540.1632-0.5464-0.53410.08150.02380.066-0.02511.1021-0.18130.713846.0693-4.889930.002
270.4450.6252-0.60433.83240.00455.22050.3832-2.19441.16781.2327-1.30860.9117-0.4912-0.78150.44830.5913-0.33390.12170.9594-0.50010.829356.32790.713836.3559
282.558-0.5067-1.72955.2011-1.15191.8914-0.1894-0.80070.20130.5669-0.04730.6075-0.0609-0.82990.04320.3041-0.08720.03710.5686-0.03040.294853.7215-11.245734.7439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 122 through 174 )A122 - 174
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 243 )A175 - 243
3X-RAY DIFFRACTION3chain 'A' and (resid 244 through 283 )A244 - 283
4X-RAY DIFFRACTION4chain 'A' and (resid 284 through 325 )A284 - 325
5X-RAY DIFFRACTION5chain 'A' and (resid 326 through 345 )A326 - 345
6X-RAY DIFFRACTION6chain 'A' and (resid 346 through 369 )A346 - 369
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 190 )B122 - 190
8X-RAY DIFFRACTION8chain 'B' and (resid 191 through 303 )B191 - 303
9X-RAY DIFFRACTION9chain 'B' and (resid 304 through 336 )B304 - 336
10X-RAY DIFFRACTION10chain 'B' and (resid 337 through 369 )B337 - 369
11X-RAY DIFFRACTION11chain 'C' and (resid 122 through 138 )C122 - 138
12X-RAY DIFFRACTION12chain 'C' and (resid 139 through 240 )C139 - 240
13X-RAY DIFFRACTION13chain 'C' and (resid 241 through 325 )C241 - 325
14X-RAY DIFFRACTION14chain 'C' and (resid 326 through 369 )C326 - 369
15X-RAY DIFFRACTION15chain 'D' and (resid 122 through 138 )D122 - 138
16X-RAY DIFFRACTION16chain 'D' and (resid 139 through 164 )D139 - 164
17X-RAY DIFFRACTION17chain 'D' and (resid 165 through 182 )D165 - 182
18X-RAY DIFFRACTION18chain 'D' and (resid 183 through 243 )D183 - 243
19X-RAY DIFFRACTION19chain 'D' and (resid 244 through 272 )D244 - 272
20X-RAY DIFFRACTION20chain 'D' and (resid 273 through 292 )D273 - 292
21X-RAY DIFFRACTION21chain 'D' and (resid 293 through 345 )D293 - 345
22X-RAY DIFFRACTION22chain 'D' and (resid 346 through 369 )D346 - 369
23X-RAY DIFFRACTION23chain 'E' and (resid 122 through 174 )E122 - 174
24X-RAY DIFFRACTION24chain 'E' and (resid 175 through 260 )E175 - 260
25X-RAY DIFFRACTION25chain 'E' and (resid 261 through 289 )E261 - 289
26X-RAY DIFFRACTION26chain 'E' and (resid 290 through 303 )E290 - 303
27X-RAY DIFFRACTION27chain 'E' and (resid 304 through 325 )E304 - 325
28X-RAY DIFFRACTION28chain 'E' and (resid 326 through 369 )E326 - 369

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