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

ID or keywords:

Entry

Database: PDB / ID: 6n0r

Title

Crystal structure of Tdp1 catalytic domain in complex with compound XZ572

Components

Tyrosyl-DNA phosphodiesterase 1

Keywords

DNA 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.544 Å

Authors

Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Burke Jr., T.R. / Pommier, Y. / Waugh, D.S.

Citation

Journal: 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

Deposition	Nov 7, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6n0r.cif.gz	381.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n0/6n0r ftp://data.pdbj.org/pub/pdb/validation_reports/n0/6n0r	HTTPS FTP

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Related structure data

Related structure data	6n0nC 6n0oC 1jy1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mz0-2 6n0o-2 6die-2 6mj5-2 6n0n-2 6w7k-2 6dji-2 6dhu-1 6die-1 6n0o-1 6djf-1 6djj-1 6mz0-1 6dim-2 6mj5-1 6w7j-2 6dji-1 6n0n-1 6djh-2 6dim-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6n0nC

6n0oC

1jy1S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#55 - Jul 2004 DNA Ligase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Tyrosyl-DNA phosphodiesterase 1

B: Tyrosyl-DNA phosphodiesterase 1

hetero molecules

105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tyrosyl-DNA phosphodiesterase 1

hetero molecules

defined by author&software
Evidence: gel filtration
52.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tyrosyl-DNA phosphodiesterase 1

hetero molecules

defined by author&software
52.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

#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 / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.77 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 16, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.54→50 Å / Num. obs: 150083 / % possible obs: 99.8 % / Redundancy: 5.6 % / R_merge(I) obs: 0.055 / R_pim(I) all: 0.03 / R_rim(I) all: 0.072 / R_sym value: 0.065 / Net I/σ(I): 35.1
Reflection shell	Resolution: 1.54→1.57 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.641 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7461 / CC_1/2: 0.811 / R_pim(I) all: 0.315 / R_rim(I) all: 0.741 / R_sym value: 0.669 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1JY1

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

	R_factor	Num. reflection	% reflection
R_free	0.195	2000	1.33 %
R_work	0.17	-	-
obs	0.1703	149966	99.29 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.544→37.025 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7006	0	48	730	7784

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7552
X-RAY DIFFRACTION	f_angle_d	0.826	10307
X-RAY DIFFRACTION	f_dihedral_angle_d	5.569	6062
X-RAY DIFFRACTION	f_chiral_restr	0.056	1071
X-RAY DIFFRACTION	f_plane_restr	0.006	1321

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.544-1.5826	0.2704	133	0.2293	9795	X-RAY DIFFRACTION	93
1.5826-1.6254	0.2533	142	0.2154	10552	X-RAY DIFFRACTION	100
1.6254-1.6733	0.2067	142	0.1957	10521	X-RAY DIFFRACTION	100
1.6733-1.7273	0.231	142	0.1902	10539	X-RAY DIFFRACTION	100
1.7273-1.789	0.2381	143	0.1885	10551	X-RAY DIFFRACTION	100
1.789-1.8606	0.2003	143	0.1786	10536	X-RAY DIFFRACTION	100
1.8606-1.9453	0.1832	142	0.174	10565	X-RAY DIFFRACTION	100
1.9453-2.0479	0.1935	143	0.1734	10566	X-RAY DIFFRACTION	100
2.0479-2.1761	0.1941	144	0.173	10646	X-RAY DIFFRACTION	100
2.1761-2.3441	0.1724	143	0.1713	10616	X-RAY DIFFRACTION	100
2.3441-2.58	0.2139	144	0.1783	10634	X-RAY DIFFRACTION	100
2.58-2.9532	0.2151	145	0.1797	10751	X-RAY DIFFRACTION	100
2.9532-3.7201	0.2027	146	0.1613	10783	X-RAY DIFFRACTION	100
3.7201-37.0356	0.1627	148	0.1502	10911	X-RAY DIFFRACTION	97

Refinement TLS params.

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

ID	L11 (°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)
1	0.1011	-0.0734	0.1505	0.0633	-0.1	0.2755	-0.08	-0.1743	0.0554	0.0814	0.0678	0.0073	-0.0914	-0.2012	-0.0028	0.1738	0.0443	-0.008	0.1748	0.0065	0.1697	1.6808	-0.2396	-35.6281
2	0.1291	-0.021	-0.0244	0.1169	-0.0378	0.1219	-0.0157	-0.0071	0.0258	-0.0058	0.0295	0.037	0.0413	-0.1229	-0.0001	0.166	-0.0047	-0.0236	0.1504	0.0271	0.1736	2.836	-4.5359	-52.0465
3	0.0927	-0.0556	0.0429	0.0485	-0.0039	0.0249	0.049	0.0151	-0.0658	-0.0089	-0.05	-0.0845	0.1474	0.1646	-0.0001	0.2026	0.0317	0.0063	0.159	0.0042	0.1638	21.7793	-18.624	-45.8111
4	0.0944	-0.0223	0.0364	0.0317	-0.0339	0.0752	0.0293	0.0009	0.0307	-0.0024	-0.029	-0.0134	0.1112	0.0422	0.0005	0.1679	-0.008	-0.0111	0.1222	0.02	0.1584	16.9488	-15.4263	-42.1789
5	0.0519	0.0081	0.0241	0.0382	0.0532	0.049	0.0354	-0.0097	0.072	0.0677	-0.0585	-0.0123	0.0375	0.0467	-0	0.2021	-0.0103	0.0013	0.2059	0.048	0.2062	24.1813	-10.6358	-33.7867
6	0.0051	0.0076	0.0055	0.0105	-0.0063	0.0149	0.0006	-0.0412	0.1012	0.0513	-0.0993	-0.0719	-0.2365	0.0666	-0.0002	0.2279	-0.0034	-0.0175	0.1978	0.0524	0.213	4.2505	16.7855	-86.3331
7	0.1043	-0.0095	0.0711	0.0325	-0.0454	0.0939	-0.0264	0.2077	0.0362	-0.0599	-0.1225	-0.1743	-0.0574	0.4918	-0.0513	0.2032	-0.0149	0.0221	0.3463	0.1162	0.2323	18.9174	8.6575	-91.4992
8	0.0048	0.0174	0.0177	0.066	0.0076	0.0248	-0.0487	0.0426	0.0383	-0.0775	-0.0892	-0.1893	-0.012	0.3754	-0.0249	-0.0498	0.1469	-0.194	0.0658	0.3343	-0.1883	14.7125	6.1291	-78.3828
9	0.0268	0.0155	0.0182	0.009	-0.0129	0.0273	0.0362	-0.1207	-0.0466	0.0887	-0.0969	-0.0411	0.128	0.1076	-0.0014	0.2101	0.0347	0.0078	0.1872	0.061	0.1918	9.2129	-7.1751	-76.0672
10	0.0506	0.0177	0.0272	0.0198	0.02	0.0303	0.0506	-0.0298	-0.1061	-0.0296	-0.0122	0.0643	0.1891	-0.1887	0	0.2645	-0.0381	0.008	0.1864	0.0472	0.2053	-6.1735	-9.7508	-88.0759
11	0.0519	0.0435	0.0643	0.0332	0.0144	0.1147	0.0151	-0.026	-0.0592	-0.0674	-0.0209	-0.0195	0.2002	-0.0871	-0.0017	0.2118	0.0253	0.0189	0.1656	0.0406	0.1712	-1.3225	-5.3248	-90.1778
12	0.054	0.0237	-0.0027	0.0288	-0.0296	0.0198	-0.037	-0.036	-0.0257	-0.0515	0.0067	0.0215	0.0578	-0.1316	-0	0.1981	0.0028	0.0149	0.2479	0.0035	0.1914	-8.439	2.4113	-96.3095

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 162 through 285 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 286 through 382 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 383 through 452 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 453 through 548 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 549 through 607 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 162 through 202 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 203 through 280 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 281 through 344 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 345 through 382 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 383 through 452 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 453 through 548 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 549 through 607 )

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