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- PDB-5j3z: Crystal structure of m2hTDP2-CAT in complex with a small molecule... -

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Basic information

Entry
Database: PDB / ID: 5j3z
TitleCrystal structure of m2hTDP2-CAT 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 / 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 / manganese ion 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 / manganese ion binding / single-stranded DNA 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
Chem-6FQ / ACETATE ION / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHornyak, P. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
Cancer Research UKC6563/A16771 United Kingdom
Cancer Research UKC480/A11411 United Kingdom
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 1.2Jan 10, 2024Group: 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,01931
Polymers57,5522
Non-polymers2,46729
Water10,881604
1
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,10917
Polymers28,7761
Non-polymers1,33316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91014
Polymers28,7761
Non-polymers1,13413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.010, 42.800, 108.760
Angle α, β, γ (deg.)90.00, 94.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 28776.164 Da / Num. of mol.: 2 / Fragment: UNP residues 118-370 / Mutation: E242G, Q278R, Y321C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS
References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 6 types, 633 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C19H10N8O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris propane pH 7.5, 0.2 M sodium citrate, 20% w/v PEG3350, 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: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→42.8 Å / Num. obs: 51393 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 21.69 Å2 / CC1/2: 0.87 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 2 / % possible all: 79.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GYZ

4gyz


Resolution: 1.8→39.81 Å / Cor.coef. Fo:Fc: 0.9516 / Cor.coef. Fo:Fc free: 0.9338 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 2611 5.08 %RANDOM
Rwork0.1726 ---
obs0.174 51379 97.94 %-
Displacement parametersBiso mean: 26.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.9739 Å20 Å2-2.6923 Å2
2---0.2711 Å20 Å2
3----2.7028 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 168 604 4764
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084264HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1971SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes713HARMONIC5
X-RAY DIFFRACTIONt_it4264HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion546SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies20HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5678SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2518 149 4.79 %
Rwork0.2192 2964 -
all0.2208 3113 -
obs--80.45 %
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)
11.13280.08310.10630.9773-0.06830.6464-0.0039-0.07360.01880.026-0.0017-0.03010.03060.09310.0056-0.06430.00950.0065-0.05130.004-0.0227-12.7288-6.6721-47.9553
21.3285-0.0110.14891.1585-0.38350.643-0.0029-0.0645-0.0777-0.01990.0196-0.09240.0271-0.0309-0.0167-0.0747-0.005-0.0066-0.0441-0.0184-0.026-16.4959-6.3087-4.9932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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