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

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Basic information

Entry
Database: PDB / ID: 1rff
TitleCrystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.
Components
  • 5'-D(*AP*GP*TP*T)-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 / DNA repair / intracellular membrane-bounded organelle ...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 / DNA repair / intracellular membrane-bounded organelle / 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: 1.7 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 8, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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*T)-3'
F: 5'-D(*AP*GP*TP*T)-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)114,64910
Polymers114,0146
Non-polymers6354
Water6,179343
1
D: 5'-D(*AP*GP*TP*T)-3'
A: Tyrosyl-DNA phosphodiesterase 1
C: Topoisomerase I-Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3255
Polymers57,0073
Non-polymers3172
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*AP*GP*TP*T)-3'
B: Tyrosyl-DNA phosphodiesterase 1
E: Topoisomerase I-Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3255
Polymers57,0073
Non-polymers3172
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.076, 104.904, 193.832
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*T)-3'


Mass: 1205.841 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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: Protein/peptide Topoisomerase I-Derived Peptide


Mass: 1070.200 Da / Num. of mol.: 2 / Fragment: residues 720-727 / Mutation: L724Y / Source method: obtained synthetically
Details: THE Peptide WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE Peptide IS NATURALLY FOUND IN "Homo sapiens" (Human).
Keywords: L724Y

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Non-polymers , 3 types, 347 molecules

#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


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


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 44.84 %
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
2NaClSodium chloride11
3HEPES11
4spermine11
5H2O11
6PEG 300012
7NaClSodium chloride12
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 103225 / Num. obs: 103255 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.52 % / Rsym value: 0.071 / Net I/σ(I): 21.04
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.482 / % possible all: 64.6
Reflection
*PLUS
Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 64.6 % / Rmerge(I) obs: 0.482

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jy1

1jy1


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.321 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21325 5161 5 %RANDOM
Rwork0.19258 ---
all0.19364 102833 --
obs0.19364 97672 90.78 %-
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: 24.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--2 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6933 102 34 343 7412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217300
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9579925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545857
X-RAY DIFFRACTIONr_chiral_restr0.1020.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025477
X-RAY DIFFRACTIONr_nbd_refined0.2050.33160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5775
X-RAY DIFFRACTIONr_metal_ion_refined0.10.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.56
X-RAY DIFFRACTIONr_mcbond_it1.74534326
X-RAY DIFFRACTIONr_mcangle_it2.75446974
X-RAY DIFFRACTIONr_scbond_it2.82442974
X-RAY DIFFRACTIONr_scangle_it4.2962951
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 280
Rwork0.32 4971
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.335

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