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- PDB-7ufy: Crystal structure of TDP1 complexed with compound XZ766 -

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Basic information

Entry
Database: PDB / ID: 7ufy
TitleCrystal structure of TDP1 complexed with compound XZ766
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE / phosphodiesterase / DNA BINDING PROTEIN
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
Chem-N8I / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 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)105,59811
Polymers104,2532
Non-polymers1,3459
Water14,556808
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8306
Polymers52,1261
Non-polymers7045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7685
Polymers52,1261
Non-polymers6424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.813, 104.732, 193.154
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-N8I / [(4-{[(4S)-2,7-diphenylimidazo[1,2-a]pyridin-3-yl]amino}phenyl)methyl]phosphonic acid


Mass: 455.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H22N3O3P / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 1.58→50 Å / Num. obs: 137386 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Net I/σ(I): 35.8
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2 / Num. unique obs: 6750 / CC1/2: 0.848 / CC star: 0.958 / Rpim(I) all: 0.304 / Rrim(I) all: 0.738 / % possible all: 99.6

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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: 1.584→44.271 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1934 6803 4.96 %
Rwork0.1656 130444 -
obs0.1669 137247 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.4 Å2 / Biso mean: 30.479 Å2 / Biso min: 12.06 Å2
Refinement stepCycle: final / Resolution: 1.584→44.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 94 808 7903
Biso mean--42.71 42.62 -
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 (%)
1.5843-1.60230.27321850.2473356183
1.6023-1.62110.26762160.2364320100
1.6211-1.64090.27222280.2194326100
1.6409-1.66160.21972300.19424385100
1.6616-1.68350.22782370.18634242100
1.6835-1.70660.22382520.18594319100
1.7066-1.7310.20932300.17734329100
1.731-1.75680.21192440.17564294100
1.7568-1.78420.20222280.17224369100
1.7842-1.81350.20872220.1684280100
1.8135-1.84480.20662280.16864384100
1.8448-1.87830.19062070.16154329100
1.8783-1.91440.20862090.15764364100
1.9144-1.95350.18372120.15784334100
1.9535-1.9960.18842500.15424375100
1.996-2.04240.17562100.15384303100
2.0424-2.09350.19572130.15524400100
2.0935-2.15010.1752160.16194367100
2.1501-2.21340.17942300.15154342100
2.2134-2.28480.18022280.16034370100
2.2848-2.36650.20022370.16534399100
2.3665-2.46120.18692150.16734356100
2.4612-2.57320.19552180.16794394100
2.5732-2.70890.20412320.174396100
2.7089-2.87860.19992460.17634385100
2.8786-3.10080.19462260.17644443100
3.1008-3.41270.20152610.16514391100
3.4127-3.90630.17892340.14984475100
3.9063-4.92050.16822200.14034529100
4.9205-44.270.19862390.1878468399
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)
11.9885-0.38850.37530.3511-0.34240.7852-0.1026-0.10310.33040.0586-0.0134-0.1058-0.2601-0.0310.13220.2060.0116-0.03140.1231-0.01130.214510.60356.4063-36.8217
21.655-0.16150.05161.6402-0.13522.0367-0.0991-0.2791-0.03870.1470.12860.21310.0162-0.3521-0.02610.1230.03110.00240.19210.01950.1656-3.2313-3.3114-35.0327
31.56190.0790.30320.636-0.03512.2636-0.06270.08350.1467-0.04380.05220.1081-0.1426-0.28910.00430.10760.0174-0.01910.10050.00650.15620.3065-0.1456-49.1514
41.425-0.36410.4181.1263-0.49941.780.09730.2277-0.2456-0.1739-0.0433-0.00770.36650.1355-0.01610.19010.0039-0.00720.1248-0.02760.18613.5848-15.88-53.4404
51.08670.0750.40970.16130.05711.2160.0504-0.0425-0.14530.0345-0.0136-0.01620.26150.0571-0.02380.1620.0101-0.01170.090.01010.179117.8451-15.2972-40.1772
61.4354-0.11360.16870.5272-0.25674.97940.0333-0.0226-0.01630.152-0.0687-0.0432-0.08110.20950.04220.1025-0.0003-0.00950.14170.00420.19224.1128-10.1931-34.1473
73.0050.14131.05490.72970.14662.6304-0.1694-0.03080.52730.0576-0.1553-0.0758-0.73780.11470.28680.2929-0.0233-0.03370.20970.06820.24264.483616.6765-85.6051
81.9123-0.1420.35541.0457-0.55452.4252-0.05610.39270.1378-0.1109-0.1551-0.2425-0.20230.74840.07850.1661-0.05620.00440.39220.12260.215415.73938.7821-87.7737
92.2450.33140.42690.99020.17722.57660.05810.0484-0.19870.0529-0.091-0.14650.34450.46920.01970.16370.06850.00350.27570.07660.165513.4665-3.612-76.2027
101.4853-0.27810.45020.68560.26942.57630.0528-0.1924-0.30790.04390.00440.1170.7305-0.3882-0.02110.2708-0.08110.01080.25850.03820.2048-6.4027-9.8332-88.0476
110.9570.0030.44210.4013-0.32863.00350.03740.0899-0.1527-0.0996-0.0342-0.00420.4337-0.145-0.00390.1852-0.00570.01450.20110.01580.1724-1.3953-5.5205-90.0347
120.86040.12150.16120.6643-0.77444.5104-0.0202-0.03970.0007-0.0498-0.02620.0565-0.0662-0.49760.05310.13540.0082-0.00060.32340.00660.2039-8.35452.2502-95.7452
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 343 )A286 - 343
4X-RAY DIFFRACTION4chain 'A' and (resid 344 through 436 )A344 - 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 318 )B203 - 318
9X-RAY DIFFRACTION9chain 'B' and (resid 319 through 382 )B319 - 382
10X-RAY DIFFRACTION10chain 'B' and (resid 383 through 452 )B383 - 452
11X-RAY DIFFRACTION11chain 'B' and (resid 453 through 548 )B453 - 548
12X-RAY DIFFRACTION12chain 'B' and (resid 549 through 608 )B549 - 608

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