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- PDB-6w4r: Structure of Tdp1 catalytic domain in complex with inhibitor XZ633p -

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Basic information

Entry
Database: PDB / ID: 6w4r
TitleStructure of Tdp1 catalytic domain in complex with inhibitor XZ633p
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsDNA BINDING PROTEIN / HYDROLASE/INHIBITOR / phosphodiesterase / inhibitor / cancer drug target / 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 / 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
Similarity search - Domain/homology
Chem-SZV / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S.
CitationJournal: To Be Published
Title: Tdp1 catalytic domain
Authors: Lountos, G.T. / Waugh, D.S.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)105,55310
Polymers104,2532
Non-polymers1,3008
Water12,574698
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8505
Polymers52,1261
Non-polymers7244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7035
Polymers52,1261
Non-polymers5774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.719, 105.624, 194.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SZV / 4-{[2-(2-hydroxyphenyl)imidazo[1,2-a]pyrazin-3-yl]amino}benzene-1,2-dicarboxylic acid


Mass: 390.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.68 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.819→50 Å / Num. obs: 92596 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Χ2: 0.961 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.819-1.855.80.93545920.7440.4241.0290.78799.9
1.85-1.896.70.9145610.8510.3810.9870.777100
1.89-1.926.70.91145790.7770.3820.9890.874100
1.92-1.966.80.76145300.9150.3150.8240.817100
1.96-26.80.58946230.9130.2450.6390.819100
2-2.056.70.51345480.9210.2150.5570.822100
2.05-2.16.70.39745730.9580.1660.4310.845100
2.1-2.166.60.35546270.9610.150.3860.85299.9
2.16-2.226.60.30145380.9770.1260.3270.85299.9
2.22-2.296.40.32945960.9240.1410.3581.299.8
2.29-2.376.40.20846460.9880.0880.2270.881100
2.37-2.476.30.17845750.9720.0780.1950.93299.8
2.47-2.585.50.14545770.9730.0690.1610.93899.3
2.58-2.726.80.12246260.9940.0510.1321.00999.9
2.72-2.897.10.10246280.9930.0410.111.072100
2.89-3.1170.07846750.9960.0320.0851.142100
3.11-3.436.90.06346520.9960.0260.0681.276100
3.43-3.926.70.05247140.9960.0220.0561.32999.9
3.92-4.945.80.03847440.9970.0170.0421.0999.5
4.94-506.50.03449920.9980.0150.0370.85899.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DHU

6dhu


Resolution: 1.819→48.164 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.93
RfactorNum. reflection% reflection
Rfree0.2153 4438 4.88 %
Rwork0.182 --
obs0.1836 90975 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.2 Å2 / Biso mean: 24.1507 Å2 / Biso min: 4.97 Å2
Refinement stepCycle: final / Resolution: 1.819→48.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7002 0 91 698 7791
Biso mean--32.4 32.92 -
Num. residues----876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8195-1.84010.321250.2451225877
1.8401-1.86180.25531300.2218243886
1.8618-1.88450.25551330.2226264691
1.8845-1.90830.26171440.2144277595
1.9083-1.93340.25941320.2176281998
1.9334-1.95990.25041460.2215288999
1.9599-1.98790.24021490.21542948100
1.9879-2.01760.26421410.21692851100
2.0176-2.04910.30021400.22112936100
2.0491-2.08270.24981530.20212917100
2.0827-2.11860.23071600.20312876100
2.1186-2.15720.2541370.20222970100
2.1572-2.19870.20411620.19212871100
2.1987-2.24350.23481480.19562899100
2.2435-2.29230.23631630.20272910100
2.2923-2.34560.25831520.19392907100
2.3456-2.40430.23571600.19322897100
2.4043-2.46930.2421580.1892924100
2.4693-2.5420.23771460.1916290999
2.542-2.6240.2351400.19062937100
2.624-2.71780.23031350.18162954100
2.7178-2.82660.22631550.192908100
2.8266-2.95520.19921480.19162984100
2.9552-3.1110.27391590.19282960100
3.111-3.30590.22721700.17882942100
3.3059-3.5610.19981340.17192994100
3.561-3.91930.1781480.15922977100
3.9193-4.4860.15381430.1363028100
4.486-5.65050.15711610.1403301799
5.6505-48.1640.1631660.17333196100

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