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- PDB-6mj5: Crystal structure of Tdp1 catalytic domain in complex with compou... -

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Basic information

Entry
Database: PDB / ID: 6mj5
TitleCrystal structure of Tdp1 catalytic domain in complex with compound XZ519
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsDNA BINDING PROTEIN / Hydrolase / fragment based drug design / anti-cancer drug design
Function / homology
Function and homology information


3'-tyrosyl-DNA phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / single strand break repair / 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 / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / single strand break repair / 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
4-hydroxy-8-nitroquinoline-3-carboxylic acid / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 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
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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)104,8579
Polymers104,0792
Non-polymers7797
Water10,449580
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4605
Polymers52,0391
Non-polymers4204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3984
Polymers52,0391
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.156, 105.686, 193.984
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: 52039.258 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JTA / 4-hydroxy-8-nitroquinoline-3-carboxylic acid


Mass: 234.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 50.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein 22 mg/mL 0.1M 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 83875 / % possible obs: 95 % / Redundancy: 6.5 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Rsym value: 0.104 / Net I/σ(I): 25.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4046 / CC1/2: 0.817 / Rpim(I) all: 0.342 / Rrim(I) all: 0.873 / Rsym value: 0.801 / % possible all: 93.8

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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: 1.853→36.42 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2183 2000 2.39 %
Rwork0.1775 --
obs0.1785 83777 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.853→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 54 580 7632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067531
X-RAY DIFFRACTIONf_angle_d0.8310274
X-RAY DIFFRACTIONf_dihedral_angle_d5.3786041
X-RAY DIFFRACTIONf_chiral_restr0.0561066
X-RAY DIFFRACTIONf_plane_restr0.0061313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8529-1.89920.29411300.24025313X-RAY DIFFRACTION88
1.8992-1.95050.29661360.23045588X-RAY DIFFRACTION91
1.9505-2.00790.26921370.2145589X-RAY DIFFRACTION91
2.0079-2.07270.25051370.20685620X-RAY DIFFRACTION92
2.0727-2.14680.2561390.19685644X-RAY DIFFRACTION92
2.1468-2.23280.24741370.19295645X-RAY DIFFRACTION92
2.2328-2.33440.24751400.18735680X-RAY DIFFRACTION93
2.3344-2.45740.25941410.18715764X-RAY DIFFRACTION94
2.4574-2.61130.24431440.18745882X-RAY DIFFRACTION95
2.6113-2.81290.1951470.19286018X-RAY DIFFRACTION97
2.8129-3.09580.26251500.19316144X-RAY DIFFRACTION99
3.0958-3.54350.21931520.1716218X-RAY DIFFRACTION100
3.5435-4.46310.15951530.13986255X-RAY DIFFRACTION100
4.4631-36.42740.18111570.15786417X-RAY DIFFRACTION98

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