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- PDB-8uv1: Structure of TDP1 complexed with compound IB01 -

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Basic information

Entry
Database: PDB / ID: 8uv1
TitleStructure of TDP1 complexed with compound IB01
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsDNA BINDING PROTEIN / phosphodiesterase / drug target / cancer
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
Similarity search - Domain/homology
: / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Barakat, I. / Wang, W. / Agama, K. / Al Mahmud, M.R. / Pommier, Y. / Burke, T.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Structure of TDP1 complexed with compound IB01
Authors: Lountos, G.T. / Zhao, X.Z. / Barakat, I. / Wang, W. / Agama, K. / Al Mahmud, M.R. / Pommier, Y. / Burke, T.R.
History
DepositionNov 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)106,27511
Polymers104,2532
Non-polymers2,0239
Water10,287571
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0025
Polymers52,1261
Non-polymers8764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2736
Polymers52,1261
Non-polymers1,1475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.958, 105.022, 193.038
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 / Plasmid: pDN2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-XK6 / 8-(fluorosulfonyl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid


Mass: 271.222 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H6FNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 49.36 %
Crystal growTemperature: 293 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 89424 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rpim(I) all: 0.034 / Rsym value: 0.084 / Net I/σ(I): 18.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4219 / CC1/2: 0.865 / CC star: 0.963 / Rpim(I) all: 0.252 / Rsym value: 0.608 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→43.851 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 4401 4.93 %
Rwork0.1629 --
obs0.1644 89336 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→43.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6970 0 130 571 7671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067598
X-RAY DIFFRACTIONf_angle_d0.83210380
X-RAY DIFFRACTIONf_dihedral_angle_d6.4786019
X-RAY DIFFRACTIONf_chiral_restr0.0551061
X-RAY DIFFRACTIONf_plane_restr0.0061316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8303-1.85110.25831370.20312582X-RAY DIFFRACTION90
1.8511-1.87290.24041310.19582652X-RAY DIFFRACTION95
1.8729-1.89580.23961130.1842740X-RAY DIFFRACTION96
1.8958-1.91980.21951530.17932730X-RAY DIFFRACTION97
1.9198-1.9450.22451340.18072775X-RAY DIFFRACTION97
1.945-1.97170.21651190.17892770X-RAY DIFFRACTION98
1.9717-1.99980.21391420.17682809X-RAY DIFFRACTION98
1.9998-2.02970.23631600.17182721X-RAY DIFFRACTION98
2.0297-2.06140.20831440.16772794X-RAY DIFFRACTION98
2.0614-2.09520.19171430.16012820X-RAY DIFFRACTION99
2.0952-2.13130.1911300.15942805X-RAY DIFFRACTION99
2.1313-2.17010.21271540.16492829X-RAY DIFFRACTION99
2.1701-2.21180.18681340.15752802X-RAY DIFFRACTION99
2.2118-2.2570.2051400.16092847X-RAY DIFFRACTION99
2.257-2.3060.25141340.16352826X-RAY DIFFRACTION99
2.306-2.35970.19281560.16042845X-RAY DIFFRACTION100
2.3597-2.41870.18051590.16562844X-RAY DIFFRACTION100
2.4187-2.48410.1951600.16092831X-RAY DIFFRACTION100
2.4841-2.55720.22321430.17252852X-RAY DIFFRACTION100
2.5572-2.63970.22281540.16292878X-RAY DIFFRACTION100
2.6397-2.7340.2161410.16332844X-RAY DIFFRACTION100
2.734-2.84350.19991210.16982909X-RAY DIFFRACTION100
2.8435-2.97290.20421620.16882878X-RAY DIFFRACTION100
2.9729-3.12960.19281530.17672888X-RAY DIFFRACTION100
3.1296-3.32560.19491590.16562901X-RAY DIFFRACTION100
3.3256-3.58220.18371650.1592863X-RAY DIFFRACTION100
3.5822-3.94250.15911490.14862894X-RAY DIFFRACTION100
3.9425-4.51250.15221700.1342946X-RAY DIFFRACTION100
4.5125-5.68330.17191680.14532946X-RAY DIFFRACTION100
5.6833-43.80.18241730.18573114X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6934-0.18790.39440.7235-0.091.7311-0.0716-0.16470.10040.05110.01970.0796-0.0995-0.24380.04520.12480.0175-0.00760.0994-0.00150.13581.55980.4286-40.2358
21.6398-0.50530.4811.53-0.52241.74370.09850.2412-0.2714-0.2358-0.0556-0.02730.36850.142-0.00070.2096-0.0020.00390.1154-0.01980.172813.8673-15.6184-53.3816
31.4545-0.10720.45110.3632-0.05261.82540.0112-0.1257-0.12910.02980.0005-0.03780.2290.15770.0140.14360.01650.00180.09340.02360.146720.5219-13.4418-37.9226
41.71240.37740.37991.0485-0.46321.9299-0.02790.44880.1738-0.079-0.2149-0.2508-0.15660.50060.1240.2-0.02070.00610.35610.1640.230213.630711.3875-89.6523
51.5449-0.00020.62330.6033-0.21842.51550.0123-0.0291-0.24030.0427-0.0842-0.06080.36090.08580.06560.18350.03370.05090.18330.06940.19595.2769-3.117-81.3096
61.17540.20620.22750.4694-0.34712.7969-0.03160.0954-0.1902-0.06760.0002-0.00140.3932-0.27840.00280.1877-0.01240.03250.18850.0160.1841-4.6428-2.8052-92.49
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 343 )
2X-RAY DIFFRACTION2chain 'A' and (resid 344 through 436 )
3X-RAY DIFFRACTION3chain 'A' and (resid 437 through 607 )
4X-RAY DIFFRACTION4chain 'B' and (resid 162 through 280 )
5X-RAY DIFFRACTION5chain 'B' and (resid 281 through 452 )
6X-RAY DIFFRACTION6chain 'B' and (resid 453 through 607 )

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