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- PDB-6n0n: Crystal structure of Tdp1 catalytic domain in complex with compou... -

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Basic information

Entry
Database: PDB / ID: 6n0n
TitleCrystal structure of Tdp1 catalytic domain in complex with compound XZ574
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-methylbenzene-1,2-dicarboxylic acid / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.477 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
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 1.1Oct 11, 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

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)105,08011
Polymers104,2532
Non-polymers8279
Water15,655869
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5095
Polymers52,1261
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5716
Polymers52,1261
Non-polymers4445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.927, 105.202, 193.743
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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-KAY / 4-methylbenzene-1,2-dicarboxylic acid


Mass: 180.157 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H8O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: 1.477→50 Å / Num. obs: 171042 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Rsym value: 0.066 / Net I/σ(I): 38.3
Reflection shellResolution: 1.477→1.51 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8405 / CC1/2: 0.834 / Rpim(I) all: 0.285 / Rrim(I) all: 0.724 / Rsym value: 0.663 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JY1

1jy1


Resolution: 1.477→36.979 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.61
RfactorNum. reflection% reflection
Rfree0.175 2000 1.17 %
Rwork0.1634 --
obs0.1635 170920 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.477→36.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 54 869 7921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077585
X-RAY DIFFRACTIONf_angle_d0.8510353
X-RAY DIFFRACTIONf_dihedral_angle_d6.4094359
X-RAY DIFFRACTIONf_chiral_restr0.0861072
X-RAY DIFFRACTIONf_plane_restr0.0061329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4767-1.51360.24581340.220511375X-RAY DIFFRACTION95
1.5136-1.55460.19051420.199511925X-RAY DIFFRACTION100
1.5546-1.60030.20131420.189712006X-RAY DIFFRACTION100
1.6003-1.6520.18851420.175911988X-RAY DIFFRACTION100
1.652-1.7110.1641420.17112042X-RAY DIFFRACTION100
1.711-1.77950.20671430.167512041X-RAY DIFFRACTION100
1.7795-1.86050.19211420.163412028X-RAY DIFFRACTION100
1.8605-1.95860.18811430.166412041X-RAY DIFFRACTION100
1.9586-2.08130.18361440.163912137X-RAY DIFFRACTION100
2.0813-2.2420.17141430.161512071X-RAY DIFFRACTION100
2.242-2.46750.17171440.167412153X-RAY DIFFRACTION100
2.4675-2.82450.20621440.172112201X-RAY DIFFRACTION100
2.8245-3.55810.16481460.16312328X-RAY DIFFRACTION100
3.5581-36.99050.15381490.146912584X-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)
11.4594-0.1054-0.57640.9322-0.3692.2089-0.0408-0.2213-0.13820.0577-0.1334-0.18960.19930.44690.10520.18070.031-0.0080.26830.10740.197713.6186-11.2792-6.9509
21.29790.5015-1.39681.2484-1.18444.1427-0.13120.0041-0.1591-0.1419-0.101-0.18960.24860.25520.22990.13280.00670.00910.18040.06290.182710.1287-9.5612-19.4104
31.1407-0.0638-0.57340.5624-0.10972.3740.09570.10670.2322-0.0379-0.0821-0.0485-0.45020.060.01250.2273-0.0457-0.02290.17330.07060.20956.17497.5004-17.682
40.8125-0.0798-0.33120.3111-0.32742.16390.0178-0.0630.15940.0915-0.0115-0.0336-0.3453-0.1069-0.01350.2031-0.008-0.01870.16790.01740.1798-2.31844.4402-5.074
51.1531-0.32830.38610.516-0.91983.7928-0.0414-0.02810.01780.0620.02010.03120.0339-0.2853-0.00750.1432-0.01690.00290.22420.00630.1824-8.5152-2.2694-0.8129
61.31280.2213-0.30241.1456-0.52231.4151-0.10040.199-0.0933-0.09630.06620.08260.1386-0.240.02280.1598-0.0390.00180.16-0.00890.14541.78450.063-61.2031
71.25260.0654-0.39740.784-0.01872.591-0.0978-0.017-0.21970.0276-0.00950.07420.2406-0.21610.09160.1297-0.00880.0240.10050.00950.16745.287-3.4362-48.9956
81.50220.447-0.0260.9073-0.19081.54470.0312-0.13180.09380.1239-0.00680.079-0.1714-0.1331-0.02580.14170.02570.0260.12470.01790.13981.47288.2203-42.8701
91.39950.1558-0.71320.8556-0.16921.58020.0581-0.17810.18370.1517-0.0773-0.0431-0.31690.20030.0180.199-0.028-0.00670.14020.00470.184621.720618.4128-51.0938
100.9443-0.0456-0.40780.238-0.04311.09280.05330.03950.1016-0.0035-0.0267-0.0015-0.2142-0.00740.00080.16620.00560.00990.10180.01920.159716.731415.3947-54.584
111.57790.0653-0.39070.2895-0.04633.14250.05790.0925-0.0256-0.1399-0.0708-0.030.05690.1350.03320.1390.00010.00060.14410.02010.188224.019410.6325-63.1272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 285 )
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 318 )
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 436 )
4X-RAY DIFFRACTION4chain 'A' and (resid 437 through 548 )
5X-RAY DIFFRACTION5chain 'A' and (resid 549 through 607 )
6X-RAY DIFFRACTION6chain 'B' and (resid 162 through 285 )
7X-RAY DIFFRACTION7chain 'B' and (resid 286 through 318 )
8X-RAY DIFFRACTION8chain 'B' and (resid 319 through 382 )
9X-RAY DIFFRACTION9chain 'B' and (resid 383 through 452 )
10X-RAY DIFFRACTION10chain 'B' and (resid 453 through 548 )
11X-RAY DIFFRACTION11chain 'B' and (resid 549 through 607 )

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