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- PDB-5inm: Mouse Tdp2 protein, apo state with variable DNA-binding grasp con... -

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Basic information

Entry
Database: PDB / ID: 5inm
TitleMouse Tdp2 protein, apo state with 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: 2.4 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)145,00413
Polymers144,5265
Non-polymers4788
Water6,521362
1
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0223
Polymers28,9051
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9302
Polymers28,9051
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0012
Polymers28,9051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0263
Polymers28,9051
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0263
Polymers28,9051
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.851, 113.445, 114.959
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.: 5 / 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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14-18% PEG3350, 100mM HEPES, 200 mM lithium sulfate, and 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: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 49969 / % possible obs: 98 % / Redundancy: 4.2 % / Biso Wilson estimate: 37.16 Å2 / Rmerge(I) obs: 0.124 / Χ2: 0.996 / Net I/av σ(I): 9.8 / Net I/σ(I): 6.6 / Num. measured all: 208499
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.493.60.518194.2
2.49-2.594.10.464198.1
2.59-2.74.30.362199.6
2.7-2.854.40.275199.8
2.85-3.024.40.229199.7
3.02-3.264.30.163199.5
3.26-3.584.30.121199
3.58-4.14.20.099198.1
4.1-5.174.10.083197
5.17-504.10.078195

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Processing

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

4gz1


Resolution: 2.4→48.815 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2538 5.09 %random
Rwork0.1789 ---
obs0.1816 49887 97.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.38 Å2 / Biso mean: 47.4644 Å2 / Biso min: 11.61 Å2
Refinement stepCycle: final / Resolution: 2.4→48.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9593 0 25 365 9983
Biso mean--73.13 38.3 -
Num. residues----1208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059885
X-RAY DIFFRACTIONf_angle_d0.81413350
X-RAY DIFFRACTIONf_chiral_restr0.0311481
X-RAY DIFFRACTIONf_plane_restr0.0031708
X-RAY DIFFRACTIONf_dihedral_angle_d11.333653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3726-2.41820.33391130.23842049216277
2.4182-2.46760.32231210.22972586270796
2.4676-2.52130.27431260.22572623274998
2.5213-2.57990.29841300.21622657278799
2.5799-2.64440.27111640.20526332797100
2.6444-2.71590.24651420.200126742816100
2.7159-2.79580.26211530.193626822835100
2.7958-2.8860.25241430.198326812824100
2.886-2.98920.30481380.204226832821100
2.9892-3.10880.23731310.194527032834100
3.1088-3.25030.24711480.18922657280599
3.2503-3.42160.23971320.17742696282899
3.4216-3.63590.20861430.16462671281499
3.6359-3.91660.20271490.15582678282798
3.9166-4.31050.20241440.14942642278697
4.3105-4.93370.17931490.13572667281697
4.9337-6.2140.20941560.1762676283297
6.214-48.82560.22681560.19562691284793

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