[English] 日本語
Yorodumi
- PDB-5inn: Mouse Tdp2 D358N protein, apo state with increased disorder among... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more