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- PDB-4f1h: Crystal structure of TDP2 from Danio rerio complexed with a singl... -

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Basic information

Entry
Database: PDB / ID: 4f1h
TitleCrystal structure of TDP2 from Danio rerio complexed with a single strand DNA
Components
  • (Tyrosyl-DNA phosphodiesterase ...) x 2
  • DNA (5'-D(P*TP*GP*CP*AP*G)-3')
KeywordsHydrolase/DNA / 5'-tyrosyl DNA phosphodiesterase / Hydrolase-DNA complex
Function / homology
Function and homology information


tyrosyl-DNA phosphodiesterase activity / convergent extension involved in gastrulation / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / determination of left/right symmetry / gastrulation / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / double-strand break repair ...tyrosyl-DNA phosphodiesterase activity / convergent extension involved in gastrulation / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / determination of left/right symmetry / gastrulation / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / double-strand break repair / single-stranded DNA binding / manganese ion binding / magnesium ion binding / DNA binding / 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
PHOSPHATE ION / DNA / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.662 Å
AuthorsShi, K. / Kurahashi, K. / Aihara, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Authors: Shi, K. / Kurahashi, K. / Gao, R. / Tsutakawa, S.E. / Tainer, J.A. / Pommier, Y. / Aihara, H.
History
DepositionMay 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*TP*GP*CP*AP*G)-3')
A: Tyrosyl-DNA phosphodiesterase 2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1069
Polymers58,6193
Non-polymers4886
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-57 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.918, 95.100, 104.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 1 types, 1 molecules C

#1: DNA chain DNA (5'-D(P*TP*GP*CP*AP*G)-3')


Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Tyrosyl-DNA phosphodiesterase ... , 2 types, 2 molecules AB

#2: 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 homolog


Mass: 28484.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish)
Gene: tdp2, ttrap, ttrapl, si:ch211-81e5.5, si:dkey-218n20.5
Production host: Escherichia coli (E. coli)
References: UniProt: Q5XJA0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: 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 homolog


Mass: 28613.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish)
Gene: tdp2, ttrap, ttrapl, si:ch211-81e5.5, si:dkey-218n20.5
Production host: Escherichia coli (E. coli)
References: UniProt: Q5XJA0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 4 types, 592 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA LARGE PORTION OF THE N-TERMINAL WAS NOT OBSERVED IN THE ELECTRON DENSITY

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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: 50.02 %
Crystal growTemperature: 293 K / pH: 7
Details: PEG and sodium tartrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 67804 / % possible obs: 99.4 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.662→45.871 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 2000 2.95 %
Rwork0.1635 --
obs0.1644 67729 98.41 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.239 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4902 Å20 Å20 Å2
2--1.5628 Å2-0 Å2
3----2.0531 Å2
Refinement stepCycle: LAST / Resolution: 1.662→45.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 105 29 586 4725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144433
X-RAY DIFFRACTIONf_angle_d1.5286041
X-RAY DIFFRACTIONf_dihedral_angle_d14.9491669
X-RAY DIFFRACTIONf_chiral_restr0.116664
X-RAY DIFFRACTIONf_plane_restr0.007762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6617-1.70320.29571140.29573737X-RAY DIFFRACTION80
1.7032-1.74930.28151410.25834627X-RAY DIFFRACTION99
1.7493-1.80070.23071430.21264734X-RAY DIFFRACTION100
1.8007-1.85890.24581440.19484710X-RAY DIFFRACTION100
1.8589-1.92530.26061440.17114727X-RAY DIFFRACTION100
1.9253-2.00240.19381430.1654723X-RAY DIFFRACTION100
2.0024-2.09350.19211440.16164738X-RAY DIFFRACTION100
2.0935-2.20390.17961440.15754737X-RAY DIFFRACTION100
2.2039-2.3420.20331450.16324752X-RAY DIFFRACTION100
2.342-2.52280.21691450.1644769X-RAY DIFFRACTION100
2.5228-2.77660.21191460.16124784X-RAY DIFFRACTION100
2.7766-3.17830.17521450.16584801X-RAY DIFFRACTION100
3.1783-4.0040.17331480.14124850X-RAY DIFFRACTION100
4.004-45.8890.16671540.15495040X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.7302 Å / Origin y: -2.4536 Å / Origin z: -1.7162 Å
111213212223313233
T0.1151 Å20.0003 Å20.0019 Å2-0.118 Å20.0068 Å2--0.1145 Å2
L0.0786 °2-0.1186 °2-0.0418 °2-0.1737 °20.0632 °2--0.052 °2
S-0.0173 Å °0.005 Å °-0.0091 Å °0.0113 Å °0.0055 Å °0.0111 Å °0.03 Å °0.0104 Å °0 Å °
Refinement TLS groupSelection details: all

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