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- PDB-7ufz: Crystal structure of TDP1 complexed with compound XZ768 -

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Basic information

Entry
Database: PDB / ID: 7ufz
TitleCrystal structure of TDP1 complexed with compound XZ768
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE / phosphodiesterase / DNA BINDING PROTEIN
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
Similarity search - Domain/homology
Chem-N7U / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.559 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Wang, W. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Front Chem / Year: 2022
Title: Phosphonic acid-containing inhibitors of tyrosyl-DNA phosphodiesterase 1.
Authors: Zhao, X.Z. / Wang, W. / Lountos, G.T. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke Jr., T.R.
History
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)106,22714
Polymers104,2532
Non-polymers1,97412
Water13,998777
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1838
Polymers52,1261
Non-polymers1,0577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0436
Polymers52,1261
Non-polymers9175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.889, 104.604, 193.095
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 / Plasmid: pDN2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-N7U / (4-{[(4S)-2-phenylimidazo[1,2-a]pyridin-3-yl]amino}phenyl)phosphonic acid


Mass: 365.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H16N3O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 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, 0.03 M sodium fluoride, 0.03 M sodium bromide and 0.03 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.559→50 Å / Num. obs: 142916 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 30.2
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6267 / CC1/2: 0.775 / CC star: 0.935 / Rpim(I) all: 0.286 / Rrim(I) all: 0.652 / % possible all: 87.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DHU

6dhu


Resolution: 1.559→43.831 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 6955 4.87 %
Rwork0.1708 135842 -
obs0.172 142797 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.23 Å2 / Biso mean: 28.8442 Å2 / Biso min: 9.62 Å2
Refinement stepCycle: final / Resolution: 1.559→43.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 106 777 7895
Biso mean--35.1 38.86 -
Num. residues----880
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5594-1.57710.26111890.2473374384
1.5771-1.59570.28662080.242407290
1.5957-1.61520.25571990.2401422192
1.6152-1.63560.24192440.2278434697
1.6356-1.65710.23662480.219452799
1.6571-1.67980.24072300.2044519100
1.6798-1.70380.21892230.19664538100
1.7038-1.72930.22782340.19544534100
1.7293-1.75630.23472550.18094507100
1.7563-1.78510.20692220.17694617100
1.7851-1.81590.20622310.17434488100
1.8159-1.84890.21912240.17274603100
1.8489-1.88440.22631970.16894546100
1.8844-1.92290.18382360.17084577100
1.9229-1.96470.18792320.17454526100
1.9647-2.01040.21952560.17174588100
2.0104-2.06070.19382260.16784552100
2.0607-2.11640.19022290.16444564100
2.1164-2.17870.21532450.1634579100
2.1787-2.2490.18722440.15984547100
2.249-2.32940.18482320.16424591100
2.3294-2.42260.21252380.16954581100
2.4226-2.53290.19182210.16864624100
2.5329-2.66640.18982370.17284587100
2.6664-2.83340.20342490.17084627100
2.8334-3.05220.18712380.17494637100
3.0522-3.35920.19262430.16834651100
3.3592-3.84510.18612440.1614680100
3.8451-4.84340.15352310.13974729100
4.8434-43.830.18872500.18284941100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.848-0.51630.46130.3701-0.45950.7555-0.0854-0.08510.42020.0271-0.0444-0.0769-0.22660.02650.12430.17180.0063-0.02060.0947-0.01670.211410.71636.8636-36.8175
21.95690.0926-0.04871.119-0.10112.0127-0.0487-0.2878-0.01730.07710.04670.15750.0736-0.2082-0.01570.11330.0243-0.00110.12810.00120.1418-3.1764-2.9245-35.0446
31.27930.02020.18520.4756-0.0411.846-0.04830.0780.1584-0.05330.00420.0897-0.1207-0.19480.03070.1120.0152-0.01640.06550.0060.15070.24140.291-49.2473
41.395-0.2850.39321.0337-0.4931.49070.09670.2365-0.274-0.1626-0.06430.01940.32930.13810.01440.18630.0115-0.00590.1051-0.02990.189413.914-15.9496-53.2352
51.06050.02490.35820.19550.12621.02590.0447-0.0785-0.16880.0415-0.02220.01080.21890.0571-0.00820.13940.0045-0.0080.07240.01850.155617.8282-14.8261-40.0474
61.9149-0.14450.34970.4902-0.36234.22850.0293-0.10340.0580.1535-0.074-0.0718-0.14510.22550.0610.1166-0.00410.00070.1313-0.00460.174423.9393-9.3031-34.5874
71.7910.09660.54060.86350.51962.394-0.06840.16910.46380.0428-0.2035-0.1091-0.7724-0.01720.20670.3365-0.0211-0.030.29860.1270.23953.89516.5151-86.1863
81.5369-0.29460.50690.9722-0.39972.1755-0.00790.53250.1829-0.0795-0.1905-0.2262-0.14150.82840.0850.1557-0.0270.01910.50860.15190.205116.12876.7304-84.5222
91.1877-0.1086-0.14751.95020.08662.89760.0589-0.222-0.31840.08480.0158-0.00040.9195-0.2323-0.01610.3574-0.0256-0.0090.27030.0490.20810.666-13.2846-81.4981
100.99880.06970.29640.4216-0.06713.35150.03590.0904-0.138-0.06570.0135-0.01590.4916-0.2877-0.04770.1862-0.01970.00370.26820.02450.1546-2.9075-5.6301-90.2832
110.95770.11120.31490.4678-0.853.877-0.01630.05940.0054-0.04570.00020.0263-0.0582-0.60390.02960.13230.0090.00710.39790.03160.1985-8.45621.8773-95.9905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 202 )A162 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 285 )A203 - 285
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 344 )A286 - 344
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 436 )A345 - 436
5X-RAY DIFFRACTION5chain 'A' and (resid 437 through 548 )A437 - 548
6X-RAY DIFFRACTION6chain 'A' and (resid 549 through 607 )A549 - 607
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 202 )B162 - 202
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 359 )B203 - 359
9X-RAY DIFFRACTION9chain 'B' and (resid 360 through 421 )B360 - 421
10X-RAY DIFFRACTION10chain 'B' and (resid 422 through 548 )B422 - 548
11X-RAY DIFFRACTION11chain 'B' and (resid 549 through 608 )B549 - 608

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