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

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Basic information

Entry
Database: PDB / ID: 6djj
TitleCrystal structure of Tdp1 catalytic domain in complex with compound XZ532
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE / fragment-based 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-aminobenzene-1,2-dicarboxylic acid / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.741 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)105,04911
Polymers104,2532
Non-polymers7979
Water15,961886
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4945
Polymers52,1261
Non-polymers3674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5566
Polymers52,1261
Non-polymers4295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.937, 105.142, 193.370
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 / Details (production host): pDN2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-GM7 / 4-aminobenzene-1,2-dicarboxylic acid


Mass: 181.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
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: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 105222 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Net I/σ(I): 39.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 5091 / CC1/2: 0.956 / Rpim(I) all: 0.115 / % possible all: 97.8

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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: 1.741→36.957 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 2000 1.9 %
Rwork0.1736 --
obs0.1742 105117 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.741→36.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7002 0 54 886 7942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067561
X-RAY DIFFRACTIONf_angle_d0.83510315
X-RAY DIFFRACTIONf_dihedral_angle_d5.4956058
X-RAY DIFFRACTIONf_chiral_restr0.0571070
X-RAY DIFFRACTIONf_plane_restr0.0061323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7411-1.78470.20651400.19767221X-RAY DIFFRACTION99
1.7847-1.83290.24571410.19267256X-RAY DIFFRACTION100
1.8329-1.88690.24881400.18587266X-RAY DIFFRACTION100
1.8869-1.94780.22191430.18617326X-RAY DIFFRACTION100
1.9478-2.01740.22171410.1827312X-RAY DIFFRACTION100
2.0174-2.09820.2251420.18417272X-RAY DIFFRACTION100
2.0982-2.19360.18871420.17797326X-RAY DIFFRACTION100
2.1936-2.30930.23341410.18217292X-RAY DIFFRACTION100
2.3093-2.45390.23121430.18397357X-RAY DIFFRACTION100
2.4539-2.64330.23231430.18567384X-RAY DIFFRACTION100
2.6433-2.90930.23511440.18497392X-RAY DIFFRACTION100
2.9093-3.330.18721440.17697453X-RAY DIFFRACTION100
3.33-4.19450.181450.15127470X-RAY DIFFRACTION100
4.1945-36.96530.17991510.15687790X-RAY DIFFRACTION100

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