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- PDB-5nw9: Crystal structure of the complex of Tdp1 with duplex DNA -

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Basic information

Entry
Database: PDB / ID: 5nw9
TitleCrystal structure of the complex of Tdp1 with duplex DNA
Components
  • DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')
  • Tyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE / protein-DNA complex / DNA repair / Nucleosidase / phosphotyrosine diesterase
Function / homology
Function and homology information


3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair ...3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tyrosyl-DNA phosphodiesterase I / Tyrosyl-DNA phosphodiesterase / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
Model detailsTdp1 with product of nucleoside cleavage
AuthorsRichardson, J.M. / Ruksenaite, E. / Morris, E.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBJ000884 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1.
Authors: Flett, F.J. / Ruksenaite, E. / Armstrong, L.A. / Bharati, S. / Carloni, R. / Morris, E.R. / Mackay, C.L. / Interthal, H. / Richardson, J.M.
History
DepositionMay 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 1
B: Tyrosyl-DNA phosphodiesterase 1
C: DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)112,2183
Polymers112,2183
Non-polymers00
Water1,02757
1
A: Tyrosyl-DNA phosphodiesterase 1
C: DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')

A: Tyrosyl-DNA phosphodiesterase 1
C: DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)114,9744
Polymers114,9744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_6135x,y,z1
Buried area1320 Å2
ΔGint-11 kcal/mol
Surface area18770 Å2
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,7311
Polymers54,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.010, 195.310, 50.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tyrosyl-DNA phosphodiesterase 1 / Tyr-DNA phosphodiesterase 1


Mass: 54731.195 Da / Num. of mol.: 2 / Fragment: delta 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP1 / Plasmid: pHN1894s D1-148 / Details (production host): pet15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: DNA chain DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IDT DNA synthesis / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Ammonium sulphate, 0.1M HEPES, 25% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→52.05 Å / Num. obs: 69045 / % possible obs: 99.2 % / Redundancy: 9.6 % / Net I/σ(I): 15.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1JY1

1jy1


Resolution: 2.04→52.05 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 17.861 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.186 / Details: molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 3336 4.8 %RANDOM
Rwork0.2319 ---
obs0.2338 65640 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 144.24 Å2 / Biso mean: 56.481 Å2 / Biso min: 29.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å2-0 Å2-0 Å2
2--0.12 Å2-0 Å2
3----1.49 Å2
Refinement stepCycle: final / Resolution: 2.04→52.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6894 169 0 57 7120
Biso mean---62.72 -
Num. residues----871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197306
X-RAY DIFFRACTIONr_bond_other_d0.0010.026752
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9239965
X-RAY DIFFRACTIONr_angle_other_deg0.722315616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3765856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79723.667300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.438151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0041524
X-RAY DIFFRACTIONr_chiral_restr0.0810.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218009
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021716
LS refinement shellResolution: 2.04→2.093 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 234 -
Rwork0.46 4664 -
all-4898 -
obs--97.71 %
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)
10.1308-0.07960.22620.7473-0.22330.4144-0.0222-0.00980.01640.0205-0.0001-0.0404-0.0064-0.04820.02230.1371-0.02040.0430.2743-0.05850.310526.9662793.0337.3376
21.5550.089-1.24530.34250.07121.3107-0.37480.61710.08730.35180.161-0.12390.5177-0.32660.21380.51430.0554-0.05190.41450.07630.608948.4883779.0386-1.4639
30.19950.3957-0.22131.4119-0.40020.35320.01560.1137-0.02820.30710.062-0.1851-0.0391-0.0887-0.07760.24320.0178-0.07820.1905-0.05680.328835.0449839.45441.2149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A161 - 608
2X-RAY DIFFRACTION2C-8 - 0
3X-RAY DIFFRACTION3B161 - 608

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