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- PDB-5inp: Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mn2+ complex -

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Basic information

Entry
Database: PDB / ID: 5inp
TitleMouse Tdp2 reaction product (5'-phosphorylated DNA)-Mn2+ 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 / 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
: / DNA / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.947 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)63,8298
Polymers63,2424
Non-polymers5864
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-37 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.592, 68.521, 166.899
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: 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*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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, 14-18% PEG3350, 200 mM sodium acetate, 10mM magnesium acetate. Crystal was soaked into the same condition with 5mM manganese chloride instead of magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.947→50 Å / Num. obs: 82918 / % possible obs: 97.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.75 Å2 / Rmerge(I) obs: 0.054 / Net I/av σ(I): 25.476 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-2.0220.181180.7
2.02-2.12.50.147192.5
2.1-2.23.60.124199.3
2.2-2.314.90.1071100
2.31-2.465.10.091100
2.46-2.655.20.0741100
2.65-2.916.50.0731100
2.91-3.338.70.0611100
3.33-4.28.40.0471100
4.2-507.20.04198.2

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Processing

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

4gz1


Resolution: 1.947→29.842 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.15
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 4171 5.03 %random
Rwork0.1429 ---
obs0.1442 82918 93.71 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 157.02 Å2 / Biso mean: 36.44 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 1.947→29.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 368 15 444 4821
Biso mean--52.81 44.82 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064695
X-RAY DIFFRACTIONf_angle_d1.0266461
X-RAY DIFFRACTIONf_chiral_restr0.044720
X-RAY DIFFRACTIONf_plane_restr0.004776
X-RAY DIFFRACTIONf_dihedral_angle_d15.2931811
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 (%)
1.9473-1.96940.2623860.20641460154653
1.9694-1.99260.2216980.17781774187264
1.9926-2.01690.191070.16921993210071
2.0169-2.04240.18591100.17682129223976
2.0424-2.06930.18981150.17462304241982
2.0693-2.09760.2141340.15832435256986
2.0976-2.12760.22911490.16382530267992
2.1276-2.15930.19271500.1482646279695
2.1593-2.1930.1831530.14662792294598
2.193-2.2290.18261320.140627662898100
2.229-2.26740.16971470.129128282975100
2.2674-2.30860.20071300.140128412971100
2.3086-2.3530.16081640.142927722936100
2.353-2.4010.1861550.145627572912100
2.401-2.45320.17311500.14728082958100
2.4532-2.51020.16781490.134228112960100
2.5102-2.5730.1751690.140527862955100
2.573-2.64250.17611450.140327922937100
2.6425-2.72020.17231520.144527922944100
2.7202-2.8080.17131690.13927892958100
2.808-2.90820.19891270.153528122939100
2.9082-3.02460.18981390.154428422981100
3.0246-3.16210.18481410.142527752916100
3.1621-3.32860.16241580.13627822940100
3.3286-3.53680.1511620.138128062968100
3.5368-3.80940.14031560.130128222978100
3.8094-4.19180.14071450.120927872932100
4.1918-4.79620.12531490.112427652914100
4.7962-6.03450.18351180.14312830294899
6.0345-29.84530.2071120.19292721283396
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)
12.0237-0.02740.15891.0710.02491.2550.0421-0.13630.02250.107-0.0179-0.03790.0258-0.1030.00420.1983-0.0118-0.01370.1709-0.02460.1646-11.2799-15.962613.107
21.49790.0281-0.00762.0688-0.0851.53040.08040.01410.0730.1301-0.1163-0.054-0.11110.01740.03310.2586-0.0184-0.01780.1659-0.010.172910.2001-59.499328.8157
33.2968-4.77891.65137.0978-2.2171.00790.04251.44870.4839-0.2342-0.47760.0003-0.12340.0810.14980.4775-0.0003-0.03410.71520.20530.58258.8155-37.752611.6047
42.023-1.22371.19244.6561-1.04652.12110.24450.2067-0.8810.2777-0.1854-0.33780.70961.2268-0.0450.60550.2151-0.13230.61980.02290.62725.8352-37.54959.4828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA116 - 370
2X-RAY DIFFRACTION2chain BB123 - 370
3X-RAY DIFFRACTION3chain CC1 - 9
4X-RAY DIFFRACTION4chain DD1 - 9

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