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- PDB-1rfi: Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexe... -

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Basic information

Entry
Database: PDB / ID: 1rfi
TitleCrystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC
Components
  • 5'-D(*AP*GP*TP*C)-3'
  • Topoisomerase I-Derived Peptide
  • Tyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE/DNA / Protein-DNA complex / vanadate complex / transition state mimic. / HYDROLASE-DNA COMPLEX
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
SPERMINE / VANADATE ION / DNA / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.
Citation
Journal: J.Med.Chem. / Year: 2004
Title: Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.
#1: Journal: Chem.Biol. / Year: 2003
Title: Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Insights into substrate binding and catalytic mechanism of human Tyrosyl-DNA Phosphodiesterase (Tdp1) from vanadate and tungstate-inhibited structures
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
#3: Journal: Structure / Year: 2002
Title: The crystal structure of human Tyrosyl-DNA Phosphodiesterase, Tdp1
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*AP*GP*TP*C)-3'
F: 5'-D(*AP*GP*TP*C)-3'
A: Tyrosyl-DNA phosphodiesterase 1
B: Tyrosyl-DNA phosphodiesterase 1
C: Topoisomerase I-Derived Peptide
E: Topoisomerase I-Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6109
Polymers113,1786
Non-polymers4323
Water4,378243
1
D: 5'-D(*AP*GP*TP*C)-3'
A: Tyrosyl-DNA phosphodiesterase 1
C: Topoisomerase I-Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9065
Polymers56,5893
Non-polymers3172
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*AP*GP*TP*C)-3'
B: Tyrosyl-DNA phosphodiesterase 1
E: Topoisomerase I-Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7044
Polymers56,5893
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.820, 104.832, 193.539
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 / Protein / Protein/peptide , 3 types, 6 molecules DFABCE

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


Mass: 1190.830 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Tyrosyl-DNA phosphodiesterase 1 / 3.1.4.- / Tyr-DNA phosphodiesterase 1 / TDP1


Mass: 54731.195 Da / Num. of mol.: 2 / Fragment: Residues 149-608 / Mutation: D322N, M328T, F548L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: Protein/peptide Topoisomerase I-Derived Peptide


Mass: 666.809 Da / Num. of mol.: 2 / Fragment: residues 720-724 / Mutation: L724K / Source method: obtained synthetically
Details: THE Peptide WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE Peptide IS NATURALLY FOUND IN "Homo sapiens" (Human).

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Non-polymers , 3 types, 246 molecules

#4: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#5: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG 3000, NaCl, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 300011
2NaCl11
3HEPES11
4spermine11
5H2O11
6PEG 300012
7NaCl12
8H2O12
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16.5 mg/mlprotein1drop
2250 mM1dropNaCl
315 mMTris1droppH8.2
41 mMEDTA1drop
519-21 %PEG30001reservoir
6200 mM1reservoirNaCl
710 mMspermine1reservoir
8100 mMHEPES1reservoiror MOPS, pH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 53356 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.26 % / Rsym value: 0.125 / Net I/σ(I): 12.99
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.62 / Rsym value: 0.527 / % possible all: 99.8
Reflection
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.125
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.527

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.059 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22699 2674 5.1 %RANDOM
Rwork0.1878 ---
all0.18977 52449 --
obs0.18977 49775 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.412 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--2.49 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6895 100 20 243 7258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217245
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9569853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775853
X-RAY DIFFRACTIONr_chiral_restr0.0850.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025443
X-RAY DIFFRACTIONr_nbd_refined0.2090.33196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5673
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.53
X-RAY DIFFRACTIONr_mcbond_it1.43834308
X-RAY DIFFRACTIONr_mcangle_it2.45746944
X-RAY DIFFRACTIONr_scbond_it2.52142937
X-RAY DIFFRACTIONr_scangle_it3.83562909
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 209
Rwork0.218 3602
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.167

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