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- PDB-6djh: Crystal structure of Tdp1 catalytic domain in complex with compou... -

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Basic information

Entry
Database: PDB / ID: 6djh
TitleCrystal structure of Tdp1 catalytic domain in complex with compound XZ515
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsHydrolase/Hydrolase Inhibitor / fragment-based drug design / Hydrolase-Hydrolase Inhibitor 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
Chem-GNM / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.918 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Burke Jr., T.R. / Pommier, Y. / Waugh, D.S.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.
Authors: Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S.
History
DepositionMay 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 1
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9757
Polymers104,2532
Non-polymers7225
Water10,557586
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5194
Polymers52,1261
Non-polymers3923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4563
Polymers52,1261
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.074, 105.149, 194.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 52126.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP1 / Plasmid: pDN2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-GNM / 8-bromo-4-oxo-1,4-dihydroquinoline-3-carboxylic acid


Mass: 268.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6BrNO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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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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: 49.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M MOPS/HEPES-Na pH 7.5 10% w/v PEG 8000 20% v/v ethylene glycol 0.03M sodium fluoride 0.03M sodium bromide 0.03M sodium iodide

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 78029 / % possible obs: 98.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Net I/σ(I): 28.4
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.957 / Num. unique obs: 3767 / CC1/2: 0.754 / Rpim(I) all: 0.343 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JY1

1jy1


Resolution: 1.918→37.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.42
RfactorNum. reflection% reflection
Rfree0.2303 2000 2.57 %
Rwork0.1773 --
obs0.1787 77943 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.918→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7002 0 42 586 7630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077522
X-RAY DIFFRACTIONf_angle_d0.87210268
X-RAY DIFFRACTIONf_dihedral_angle_d5.4546044
X-RAY DIFFRACTIONf_chiral_restr0.0571067
X-RAY DIFFRACTIONf_plane_restr0.0071312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9184-1.96640.29771300.244923X-RAY DIFFRACTION91
1.9664-2.01960.29181400.22185333X-RAY DIFFRACTION97
2.0196-2.0790.28081400.2185311X-RAY DIFFRACTION97
2.079-2.14610.27951390.21085291X-RAY DIFFRACTION97
2.1461-2.22280.27951400.20515313X-RAY DIFFRACTION97
2.2228-2.31180.25361410.25377X-RAY DIFFRACTION98
2.3118-2.4170.23421430.19865376X-RAY DIFFRACTION98
2.417-2.54440.30171420.19645451X-RAY DIFFRACTION99
2.5444-2.70370.25581450.19095494X-RAY DIFFRACTION100
2.7037-2.91240.25811470.18955539X-RAY DIFFRACTION100
2.9124-3.20530.21441460.18095530X-RAY DIFFRACTION100
3.2053-3.66880.19211460.15995610X-RAY DIFFRACTION100
3.6688-4.62090.18011500.13725647X-RAY DIFFRACTION100
4.6209-37.08720.21891510.16485748X-RAY DIFFRACTION98

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