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

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Basic information

Entry
Database: PDB / ID: 5nwa
TitleCrystal structure of the complex of Tdp1 with duplex DNA
Components
  • DNA (5'-D(P*AP*AP*TP*GP*CP*GP*CP*AP*TP*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 / DNA (> 10) / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
Model detailsTdp1 with product of nucleoside cleavage
AuthorsRichardson, J.M. / Ruksenaite, E. / Morris, E.R.
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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,8203
Polymers112,8203
Non-polymers00
Water00
1
A: Tyrosyl-DNA phosphodiesterase 1
C: DNA (5'-D(P*AP*AP*TP*GP*CP*GP*CP*AP*TP*TP*A)-3')

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


Theoretical massNumber of molelcules
Total (without water)116,1774
Polymers116,1774
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2
B: Tyrosyl-DNA phosphodiesterase 1


Theoretical massNumber of molelcules
Total (without water)54,7311
Polymers54,7311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.191, 198.192, 51.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / 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*AP*AP*TP*GP*CP*GP*CP*AP*TP*TP*A)-3')


Mass: 3357.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IDT DNA synthesis / Source: (synth.) synthetic construct (others)

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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: 2.46 Å3/Da / Density % sol: 50.03 %
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: 0.92819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 3.2→99.1 Å / Num. obs: 19558 / % possible obs: 100 % / Redundancy: 8.4 % / Net I/σ(I): 4.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1jy1


Resolution: 3.2→99.1 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.869 / SU B: 39.876 / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.634 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.306 952 5 %RANDOM
Rwork0.25 ---
obs0.253 17951 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.95 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å20 Å2
2---9.63 Å20 Å2
3---6.11 Å2
Refinement stepCycle: LAST / Resolution: 3.2→99.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 199 0 0 7186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197435
X-RAY DIFFRACTIONr_bond_other_d0.0020.026872
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.92210141
X-RAY DIFFRACTIONr_angle_other_deg0.954315903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43723.663303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4111524
X-RAY DIFFRACTIONr_chiral_restr0.0740.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 84 -
Rwork0.376 1270 -
obs--98.83 %

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