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- PDB-6n0d: Crystal structure of Tdp1 catalytic domain in complex with compou... -

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Basic information

Entry
Database: PDB / ID: 6n0d
TitleCrystal structure of Tdp1 catalytic domain in complex with compound XZ575
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsDNA BINDING PROTEIN / Hydrolase / fragment based drug design / anti-cancer drug design
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 / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-fluorobenzene-1,2-dicarboxylic acid / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.453 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Burke Jr., T.R. / Pommier, Y. / Waugh, D.S.
CitationJournal: To Be Published
Title: Crystal structure of Tdp1 catalytic domain in complex with compound XZ575
Authors: Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Burke Jr., T.R. / Pommier, Y. / Waugh, D.S.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)104,7456
Polymers104,2532
Non-polymers4924
Water14,340796
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3733
Polymers52,1261
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3733
Polymers52,1261
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.058, 105.429, 193.915
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-K8J / 4-fluorobenzene-1,2-dicarboxylic acid


Mass: 184.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5FO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M 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, 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-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 180688 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Rsym value: 0.071 / Net I/σ(I): 37.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2 / Num. unique obs: 6922 / CC1/2: 0.738 / Rpim(I) all: 0.357 / Rrim(I) all: 0.861 / Rsym value: 0.781 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.453→37.053 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 2000 1.11 %
Rwork0.1669 --
obs0.1672 180566 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.453→37.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 34 796 7805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057528
X-RAY DIFFRACTIONf_angle_d0.82110282
X-RAY DIFFRACTIONf_dihedral_angle_d6.4214325
X-RAY DIFFRACTIONf_chiral_restr0.0851071
X-RAY DIFFRACTIONf_plane_restr0.0061317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4533-1.48970.25631380.221512286X-RAY DIFFRACTION97
1.4897-1.52990.23311410.202312652X-RAY DIFFRACTION100
1.5299-1.5750.21941420.187812680X-RAY DIFFRACTION100
1.575-1.62580.21491420.177212685X-RAY DIFFRACTION100
1.6258-1.68390.20481420.160512653X-RAY DIFFRACTION100
1.6839-1.75130.20191420.161912674X-RAY DIFFRACTION100
1.7513-1.8310.16811420.166312700X-RAY DIFFRACTION100
1.831-1.92760.19041430.163112773X-RAY DIFFRACTION100
1.9276-2.04830.17161430.163112734X-RAY DIFFRACTION100
2.0483-2.20650.18751430.16612786X-RAY DIFFRACTION100
2.2065-2.42850.20661430.169212821X-RAY DIFFRACTION100
2.4285-2.77980.21021450.176312929X-RAY DIFFRACTION100
2.7798-3.50180.18041450.17112913X-RAY DIFFRACTION100
3.5018-37.06480.18891490.153213280X-RAY DIFFRACTION99
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)
11.9141-0.45970.32531.1077-0.55610.7868-0.1499-0.10110.39210.1011-0.0207-0.1488-0.3048-0.01930.11870.19350.0124-0.04270.14-0.00870.18210.95746.6712-37.0538
21.2245-0.09620.08651.8248-0.23871.7107-0.0936-0.2766-0.0050.1880.1050.2354-0.0225-0.3441-0.03570.11910.03870.00310.23420.00790.1393-3.4674-2.9568-35.3808
31.3326-0.10290.39170.9031-0.04042.7374-0.09830.0060.1836-0.0139-0.00750.0843-0.2649-0.20740.07580.09430.008-0.02260.10590.00280.13795.45082.4826-46.1556
41.21-0.28460.42760.6873-0.29661.28050.05080.1459-0.0669-0.1232-0.02050.05080.1472-0.0393-0.01610.131-0.0226-0.01210.12440.00640.11516.4939-10.4669-52.8581
53.43460.1492-0.38496.4428-3.81312.7170.17370.3831-0.1873-0.5293-0.02210.12540.56940.1737-0.1940.29390.04660.0150.217-0.03640.207319.8546-21.9853-53.7415
60.9137-0.05370.34630.3534-0.04361.09430.0338-0.0585-0.08940.0181-0.0187-0.00430.18630.03220.00370.129-0.0035-0.00830.11730.02280.123317.8487-15.177-40.4641
71.46930.02170.17810.3517-0.33283.64110.0511-0.08350.02170.1324-0.0574-0.0319-0.09050.1699-0.00480.1202-0.0003-0.0040.17330.01830.171324.1704-10.3682-34.1601
80.69740.23120.44610.3353-0.11081.7152-0.07740.0210.28320.0523-0.104-0.0638-0.44470.06050.1680.2215-0.0042-0.01910.19750.06160.20044.170716.7781-86.5558
91.2478-0.11780.43510.9402-0.47552.3556-0.05050.2370.0845-0.0452-0.1345-0.2238-0.10130.60250.07050.1216-0.0130.01510.3280.10550.189417.00767.4679-85.8139
101.02060.47180.1351.5650.25493.16140.0206-0.1065-0.23690.1292-0.0523-0.13420.55970.21570.03250.1930.06690.0040.2190.08190.1849.1689-7.1655-76.1453
111.3879-0.13430.44430.8010.13292.41130.0469-0.1109-0.28390.01430.02460.04360.5861-0.3344-0.05430.2389-0.05140.01620.22880.0310.1868-6.2261-9.5652-88.2923
121.03940.07990.37650.4312-0.21642.23370.0280.0579-0.179-0.0822-0.0249-0.04340.3647-0.07930.00680.17090.01110.02250.1740.02270.1524-1.1777-5.4022-90.2752
131.03780.2655-0.35810.603-1.13254.3252-0.0220.0448-0.0126-0.06390.03180.0452-0.0848-0.3083-0.04090.12730.00880.00040.26670.0110.1689-8.40482.1992-96.5959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 280 )
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 318 )
4X-RAY DIFFRACTION4chain 'A' and (resid 319 through 407 )
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 436 )
6X-RAY DIFFRACTION6chain 'A' and (resid 437 through 548 )
7X-RAY DIFFRACTION7chain 'A' and (resid 549 through 607 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 202 )
9X-RAY DIFFRACTION9chain 'B' and (resid 203 through 344 )
10X-RAY DIFFRACTION10chain 'B' and (resid 345 through 382 )
11X-RAY DIFFRACTION11chain 'B' and (resid 383 through 452 )
12X-RAY DIFFRACTION12chain 'B' and (resid 453 through 548 )
13X-RAY DIFFRACTION13chain 'B' and (resid 549 through 607 )

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