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- PDB-6dim: Crystal structure of Tdp1 catalytic domain in complex with Zenobi... -

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Basic information

Entry
Database: PDB / ID: 6dim
TitleCrystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982 from cocktail soak
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
4-hydroxyquinoline-3-carboxylic acid / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 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 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)105,00310
Polymers104,2532
Non-polymers7518
Water10,485582
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4404
Polymers52,1261
Non-polymers3133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5646
Polymers52,1261
Non-polymers4375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.111, 105.642, 194.950
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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-GJP / 4-hydroxyquinoline-3-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 93819 / % possible obs: 97.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Net I/σ(I): 29.2
Reflection shellResolution: 1.82→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4647 / CC1/2: 0.622 / Rpim(I) all: 0.501 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.81→40.988 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.08
RfactorNum. reflection% reflection
Rfree0.2267 2000 2.13 %
Rwork0.1863 --
obs0.1872 93775 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→40.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 52 582 7641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077526
X-RAY DIFFRACTIONf_angle_d0.83610264
X-RAY DIFFRACTIONf_dihedral_angle_d5.5256046
X-RAY DIFFRACTIONf_chiral_restr0.0571066
X-RAY DIFFRACTIONf_plane_restr0.0061311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.806-1.85120.33261390.28056402X-RAY DIFFRACTION96
1.8512-1.90130.29151420.24416477X-RAY DIFFRACTION98
1.9013-1.95720.29981420.24236558X-RAY DIFFRACTION98
1.9572-2.02040.28381430.22636516X-RAY DIFFRACTION99
2.0204-2.09260.24991420.21676536X-RAY DIFFRACTION98
2.0926-2.17640.27731430.20736544X-RAY DIFFRACTION98
2.1764-2.27540.24081420.20216519X-RAY DIFFRACTION98
2.2754-2.39540.23431420.20086563X-RAY DIFFRACTION98
2.3954-2.54540.25021430.20116566X-RAY DIFFRACTION98
2.5454-2.74190.23321440.19796577X-RAY DIFFRACTION98
2.7419-3.01780.27791440.20346597X-RAY DIFFRACTION98
3.0178-3.45420.2221440.18926599X-RAY DIFFRACTION98
3.4542-4.35120.2051440.15056592X-RAY DIFFRACTION97
4.3512-40.99890.16051460.15336729X-RAY DIFFRACTION95

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