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- PDB-6n0r: Crystal structure of Tdp1 catalytic domain in complex with compou... -

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Basic information

Entry
Database: PDB / ID: 6n0r
TitleCrystal structure of Tdp1 catalytic domain in complex with compound XZ572
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 / 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 / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(methylamino)benzene-1,2-dicarboxylic acid / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.544 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)104,9699
Polymers104,2532
Non-polymers7177
Water13,151730
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5866
Polymers52,1261
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3843
Polymers52,1261
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.043, 105.399, 193.590
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-K8D / 4-(methylamino)benzene-1,2-dicarboxylic acid


Mass: 195.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / 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.: 730 / 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: 49.77 %
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: 1.54→50 Å / Num. obs: 150083 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Rsym value: 0.065 / Net I/σ(I): 35.1
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7461 / CC1/2: 0.811 / Rpim(I) all: 0.315 / Rrim(I) all: 0.741 / Rsym value: 0.669 / % possible all: 99.9

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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
Resolution: 1.544→37.025 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.76
RfactorNum. reflection% reflection
Rfree0.195 2000 1.33 %
Rwork0.17 --
obs0.1703 149966 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.544→37.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 0 48 730 7784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067552
X-RAY DIFFRACTIONf_angle_d0.82610307
X-RAY DIFFRACTIONf_dihedral_angle_d5.5696062
X-RAY DIFFRACTIONf_chiral_restr0.0561071
X-RAY DIFFRACTIONf_plane_restr0.0061321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.544-1.58260.27041330.22939795X-RAY DIFFRACTION93
1.5826-1.62540.25331420.215410552X-RAY DIFFRACTION100
1.6254-1.67330.20671420.195710521X-RAY DIFFRACTION100
1.6733-1.72730.2311420.190210539X-RAY DIFFRACTION100
1.7273-1.7890.23811430.188510551X-RAY DIFFRACTION100
1.789-1.86060.20031430.178610536X-RAY DIFFRACTION100
1.8606-1.94530.18321420.17410565X-RAY DIFFRACTION100
1.9453-2.04790.19351430.173410566X-RAY DIFFRACTION100
2.0479-2.17610.19411440.17310646X-RAY DIFFRACTION100
2.1761-2.34410.17241430.171310616X-RAY DIFFRACTION100
2.3441-2.580.21391440.178310634X-RAY DIFFRACTION100
2.58-2.95320.21511450.179710751X-RAY DIFFRACTION100
2.9532-3.72010.20271460.161310783X-RAY DIFFRACTION100
3.7201-37.03560.16271480.150210911X-RAY DIFFRACTION97
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)
10.1011-0.07340.15050.0633-0.10.2755-0.08-0.17430.05540.08140.06780.0073-0.0914-0.2012-0.00280.17380.0443-0.0080.17480.00650.16971.6808-0.2396-35.6281
20.1291-0.021-0.02440.1169-0.03780.1219-0.0157-0.00710.0258-0.00580.02950.0370.0413-0.1229-0.00010.166-0.0047-0.02360.15040.02710.17362.836-4.5359-52.0465
30.0927-0.05560.04290.0485-0.00390.02490.0490.0151-0.0658-0.0089-0.05-0.08450.14740.1646-0.00010.20260.03170.00630.1590.00420.163821.7793-18.624-45.8111
40.0944-0.02230.03640.0317-0.03390.07520.02930.00090.0307-0.0024-0.029-0.01340.11120.04220.00050.1679-0.008-0.01110.12220.020.158416.9488-15.4263-42.1789
50.05190.00810.02410.03820.05320.0490.0354-0.00970.0720.0677-0.0585-0.01230.03750.0467-00.2021-0.01030.00130.20590.0480.206224.1813-10.6358-33.7867
60.00510.00760.00550.0105-0.00630.01490.0006-0.04120.10120.0513-0.0993-0.0719-0.23650.0666-0.00020.2279-0.0034-0.01750.19780.05240.2134.250516.7855-86.3331
70.1043-0.00950.07110.0325-0.04540.0939-0.02640.20770.0362-0.0599-0.1225-0.1743-0.05740.4918-0.05130.2032-0.01490.02210.34630.11620.232318.91748.6575-91.4992
80.00480.01740.01770.0660.00760.0248-0.04870.04260.0383-0.0775-0.0892-0.1893-0.0120.3754-0.0249-0.04980.1469-0.1940.06580.3343-0.188314.71256.1291-78.3828
90.02680.01550.01820.009-0.01290.02730.0362-0.1207-0.04660.0887-0.0969-0.04110.1280.1076-0.00140.21010.03470.00780.18720.0610.19189.2129-7.1751-76.0672
100.05060.01770.02720.01980.020.03030.0506-0.0298-0.1061-0.0296-0.01220.06430.1891-0.188700.2645-0.03810.0080.18640.04720.2053-6.1735-9.7508-88.0759
110.05190.04350.06430.03320.01440.11470.0151-0.026-0.0592-0.0674-0.0209-0.01950.2002-0.0871-0.00170.21180.02530.01890.16560.04060.1712-1.3225-5.3248-90.1778
120.0540.0237-0.00270.0288-0.02960.0198-0.037-0.036-0.0257-0.05150.00670.02150.0578-0.1316-00.19810.00280.01490.24790.00350.1914-8.4392.4113-96.3095
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 382 )
3X-RAY DIFFRACTION3chain 'A' and (resid 383 through 452 )
4X-RAY DIFFRACTION4chain 'A' and (resid 453 through 548 )
5X-RAY DIFFRACTION5chain 'A' and (resid 549 through 607 )
6X-RAY DIFFRACTION6chain 'B' and (resid 162 through 202 )
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 280 )
8X-RAY DIFFRACTION8chain 'B' and (resid 281 through 344 )
9X-RAY DIFFRACTION9chain 'B' and (resid 345 through 382 )
10X-RAY DIFFRACTION10chain 'B' and (resid 383 through 452 )
11X-RAY DIFFRACTION11chain 'B' and (resid 453 through 548 )
12X-RAY DIFFRACTION12chain 'B' and (resid 549 through 607 )

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