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- PDB-5j3s: Crystal structure of the catalytic domain of human tyrosyl DNA ph... -

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Basic information

Entry
Database: PDB / ID: 5j3s
TitleCrystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small molecule inhibitor
ComponentsTyrosyl-DNA phosphodiesterase 2
KeywordsHYDROLASE / tyrosyl DNA phosphodiesterase 2 catalytic domain
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
Chem-6FQ / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHornyak, P. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
CitationJournal: Biochem.J. / Year: 2016
Title: Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S. ...Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S.E. / Atack, J.R. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2072
Polymers28,8241
Non-polymers3821
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.516, 68.516, 209.505
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: 28824.314 Da / Num. of mol.: 1 / Mutation: C273S
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): B834(DE3)
References: UniProt: O95551, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-6FQ / 2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile


Mass: 382.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H10N8O2

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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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 1.2M D/L-Malic acid pH7.0, 0.1M Bis-Tris propane pH 7.0, 3% v/v DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→45.22 Å / Num. obs: 7545 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2423 / Net I/σ(I): 6.4
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.025 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J3P

5j3p


Resolution: 3.4→45.218 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.22
RfactorNum. reflection% reflection
Rfree0.2729 360 4.77 %
Rwork0.2539 --
obs0.2549 7545 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→45.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 29 0 1761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021800
X-RAY DIFFRACTIONf_angle_d0.4942458
X-RAY DIFFRACTIONf_dihedral_angle_d12.3871109
X-RAY DIFFRACTIONf_chiral_restr0.04283
X-RAY DIFFRACTIONf_plane_restr0.004314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4004-3.89220.36661130.3462393X-RAY DIFFRACTION100
3.8922-4.90280.24941070.25462433X-RAY DIFFRACTION100
4.9028-45.22230.2591400.22082359X-RAY DIFFRACTION100
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)
14.07690.45812.19671.3593-1.37733.1657-0.027-0.6932-0.2793-0.38540.043-0.2748-0.0974-1.20140.07561.3427-0.36650.0820.7440.02630.3625-11.8758-11.12179.7725
21.70270.29421.44580.08220.12753.1215-0.1562-0.135-0.54740.1726-0.22770.43352.0758-1.85220.03151.3405-0.72490.18741.5703-0.17090.6398-17.6003-16.148111.8733
33.82154.44963.21385.94494.56424.79660.2493-0.3497-0.41661.56290.0201-0.38860.4851-0.08631.40682.7853-0.610.12030.61530.0390.7872-7.3384-25.513115.7504
40.91791.64050.2134.94333.32764.57450.29420.31110.0419-0.63860.4581-0.34690.98280.45190.21461.6663-0.30220.00080.55960.05770.6933-4.7568-22.390310.331
51.6101-0.6637-0.44813.4612-0.86170.5255-0.16770.2585-0.1978-0.23570.6053-0.42921.32650.15280.04671.40820.0158-0.04830.41610.09370.58382.8872-18.79945.8519
68.33520.25923.81034.1598-1.5016.2603-0.60280.18541.41320.2814-0.2830.08080.7528-0.04430.39480.6346-0.05470.0940.57170.03170.5535-5.4945-8.70854.3877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 112 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 198 )
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 233 )
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 301 )
6X-RAY DIFFRACTION6chain 'A' and (resid 302 through 357 )

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