PDB-6ili: Crystal structure of human MTH1(G2K/D120N mutant) in complex with...

ID or keywords:

Entry

Database: PDB / ID: 6ili

Title

Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 6.5

Components

7,8-dihydro-8-oxoguanine triphosphatase

Keywords

HYDROLASE / ALPHA-BETA-ALPHA SANDWICH / DNA DAMAGE / DNA REPAIR / DNA REPLICATION

Function / homology

Function and homology information

2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.45 Å

Authors

Nakamura, T. / Waz, S. / Hirata, K. / Nakabeppu, Y. / Yamagata, Y.

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity
Authors: Waz, S. / Nakamura, T. / Hirata, K. / Koga-Ogawa, Y. / Chirifu, M. / Arimori, T. / Tamada, T. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.

History

Deposition	Oct 18, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ili.cif.gz	157.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6ili.ent.gz	125.4 KB	Display	PDB format
PDBx/mmJSON format	6ili.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	5ghiC 5ghjC 5ghmC 5ghnC 5ghoC 5ghpC 5ghqC 5ws7C C: citing same article (ref.)
Similar structure data	5ghn-1 6jvq-1 5ghj-1 5ghm-1 6qvo-1 6glg-d 5nhy-2 6ehh-2 6jvj-2 6jvi-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (6) #201 - Sep 2016 Isoprene Synthase similarity (4)

Deposited unit

A: 7,8-dihydro-8-oxoguanine triphosphatase

B: 7,8-dihydro-8-oxoguanine triphosphatase

hetero molecules

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

1

A: 7,8-dihydro-8-oxoguanine triphosphatase

hetero molecules

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

2

B: 7,8-dihydro-8-oxoguanine triphosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.071, 47.132, 123.032
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	7,8-dihydro-8-oxoguanine triphosphatase / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1 Mass: 18042.605 Da / Num. of mol.: 2 / Mutation: G2K, D120N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical	ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / 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: 1.85 Å³/Da / Density % sol: 33.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: SODIUM CITRATE, cacodylate, NACL

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 25, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.45→50 Å / Num. obs: 48166 / % possible obs: 99.3 % / Redundancy: 6.9 % / R_merge(I) obs: 0.075 / Net I/σ(I): 46
Reflection shell	Resolution: 1.45→1.48 Å / R_merge(I) obs: 0.41 / Num. unique obs: 2390

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.45→37.413 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.12

	R_factor	Num. reflection	% reflection
R_free	0.2047	2433	5.06 %
R_work	0.1745	-	-
obs	0.176	48102	99.1 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→37.413 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2542	0	64	324	2930

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	2878
X-RAY DIFFRACTION	f_angle_d	1.466	3928
X-RAY DIFFRACTION	f_dihedral_angle_d	17.077	1092
X-RAY DIFFRACTION	f_chiral_restr	0.102	406
X-RAY DIFFRACTION	f_plane_restr	0.01	504

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 (%)
1.4487-1.4783	0.2817	137	0.216	2538	X-RAY DIFFRACTION	95
1.4783-1.5104	0.2745	151	0.2003	2608	X-RAY DIFFRACTION	99
1.5104-1.5456	0.2199	137	0.1893	2656	X-RAY DIFFRACTION	99
1.5456-1.5842	0.2096	139	0.1901	2674	X-RAY DIFFRACTION	99
1.5842-1.6271	0.2457	157	0.1791	2623	X-RAY DIFFRACTION	99
1.6271-1.6749	0.2384	124	0.1893	2678	X-RAY DIFFRACTION	99
1.6749-1.729	0.2085	131	0.182	2686	X-RAY DIFFRACTION	100
1.729-1.7908	0.2449	126	0.1839	2674	X-RAY DIFFRACTION	100
1.7908-1.8625	0.2035	155	0.1881	2662	X-RAY DIFFRACTION	100
1.8625-1.9472	0.2144	148	0.1794	2693	X-RAY DIFFRACTION	100
1.9472-2.0499	0.196	144	0.1751	2700	X-RAY DIFFRACTION	100
2.0499-2.1783	0.2139	163	0.1725	2662	X-RAY DIFFRACTION	100
2.1783-2.3465	0.2176	167	0.1789	2701	X-RAY DIFFRACTION	100
2.3465-2.5826	0.2002	144	0.1845	2715	X-RAY DIFFRACTION	100
2.5826-2.9561	0.226	142	0.1827	2747	X-RAY DIFFRACTION	100
2.9561-3.7239	0.1757	118	0.1514	2799	X-RAY DIFFRACTION	100
3.7239-37.4256	0.1758	150	0.1659	2853	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	2.2705	-1.0618	0.7591	1.6145	0.5238	1.2608	-0.0129	0.1592	0.2091	-0.2917	-0.0443	0.0651	0.0506	0.0495	0.1087	0.1108	0.0155	0.0112	0.1159	0.0145	0.0906	3.092	-0.6462	-15.8387
2	2.9972	1.2354	0.0051	2.1982	-0.244	3.8183	-0.1887	-0.0749	0.2507	0.1135	0.1764	0.3731	-0.3937	-0.4647	0.0568	0.1923	0.0317	0.0137	0.1329	0.0052	0.1329	-6.3353	-17.1632	-16.2127
3	3.4413	-0.08	-0.5337	6.54	-0.2904	0.843	0.0136	-0.2495	0.0413	0.9144	0.0196	0.2364	-0.2727	0.0227	0.0103	0.2419	0.0118	0.018	0.1353	-0.005	0.0979	1.5175	-8.0757	-5.4106
4	1.6127	0.8773	-1.1764	2.4698	-1.8862	1.393	0.1203	-0.2502	-0.1853	0.2103	-0.3813	-0.1076	0.0175	0.4323	0.2603	0.2052	0.0254	0.0027	0.1835	0.0062	0.1352	5.3551	-9.9658	-13.8194
5	1.713	-0.6068	1.15	2.5642	-2.0992	1.9899	0.0612	0.0057	-0.0347	0.0709	-0.194	-0.0858	0.0828	0.0377	0.0762	0.1528	0.0219	0.0059	0.1299	-0.0095	0.1202	2.338	-2.992	-17.834
6	5.5459	-3.0673	0.6453	6.8586	-1.6198	3.4227	-0.1279	-0.9084	0.6209	0.4483	0.1196	-0.1943	-0.6313	-0.0219	0.2044	0.3473	0.0015	-0.0139	0.1559	-0.0202	0.1307	-3.758	-20.9644	-5.4514
7	1.1627	-1.0634	0.3839	3.2837	-0.766	1.8144	-0.0414	-0.0255	0.0743	0.0807	0.0874	0.0635	-0.1417	-0.2285	-0.0561	0.1373	0.0079	0.0126	0.104	0.0109	0.1115	-5.0382	-21.2608	-19.9861
8	3.2261	-1.6606	0.1594	2.5716	0.2367	1.6401	0.0573	-0.1384	-0.2055	0.1193	0.0689	0.1847	0.1404	-0.178	-0.1515	0.204	-0.0277	0.019	0.1178	0.0127	0.163	3.7379	-15.3819	-24.8179
9	4.2023	-2.6835	1.585	3.8304	-0.7525	2.2452	-0.142	-0.1334	0.0664	0.217	0.1339	-0.1085	0.066	0.0834	0.0277	0.1138	0.0022	0.0201	0.0816	-0.0013	0.0808	5.8451	-7.5664	-26.7545
10	8.2533	0.2638	-2.3171	0.5979	0.2664	1.2339	-0.0235	0.0125	0.0978	-0.0029	0.0135	0.0625	0.0433	-0.1367	-0.0201	0.1052	0.0034	-0.0139	0.135	0.0022	0.099	11.4784	8.0883	-14.2159
11	2.5738	-1.3466	-0.5026	6.9499	0.9106	2.9023	0.1056	0.1888	-0.0382	-0.1066	-0.1035	0.1784	-0.0896	-0.1875	-0.0319	0.0777	0.0065	0.0226	0.1152	0.0266	0.0793	32.7725	13.4069	-16.0279
12	0.609	-0.1032	-0.9099	0.8636	-0.3649	5.1043	0.3651	1.0419	-0.1104	-0.7625	0.1475	0.4991	-0.9344	-2.4184	-0.2905	0.3844	0.2112	0.0183	0.5846	0.1128	0.2419	22.0011	23.0248	-13.9764
13	5.6299	1.7233	2.047	7.0262	3.0052	4.3467	-0.327	0.9489	0.0406	-0.5535	0.2409	0.4953	0.0468	-0.4096	0.1313	0.1415	-0.0708	-0.0139	0.3307	0.0314	0.1695	15.2797	9.2826	-24.0188
14	6.6549	3.1222	0.4799	4.0384	-0.9483	0.5422	-0.6888	1.2544	0.8949	-0.4104	0.3322	0.1034	0.3368	-0.7059	-0.2245	0.1546	-0.0566	0.0389	0.4424	0.0012	0.1526	22.6942	9.7046	-26.0708
15	3.0102	-0.6827	-1.5027	2.762	0.3828	1.2453	-0.19	0.0501	-0.1638	-0.0694	0.1089	-0.0202	0.0049	0.0755	0.0808	0.108	0.0115	-0.0253	0.1486	-0.0003	0.085	17.822	6.6485	-14.4846
16	4.7012	-0.3891	-0.6907	5.8464	0.737	2.5926	-0.3196	0.1718	0.0242	0.1082	0.5635	0.2427	-0.279	-0.7429	0.1031	0.1994	0.0923	0.0279	0.26	0.0761	0.1215	30.5683	15.2848	-25.4009
17	5.1692	-1.3476	-0.4392	1.9667	-0.1899	2.7955	0.0968	-0.0613	0.1464	-0.0586	-0.0653	0.0401	-0.2367	-0.0996	0.0024	0.123	0.0124	0.0074	0.0975	0.0043	0.1135	31.6396	17.0506	-11.3778
18	2.5037	-1.7383	-0.0686	3.002	-1.72	1.6821	0.0189	-0.0541	0.0735	0.338	-0.0836	-0.1878	-0.4241	0.2731	0.02	0.1208	-0.1023	-0.0371	0.3052	0.0871	0.1551	25.9945	7.8325	-5.9609
19	6.0207	-3.3	-2.5318	4.4566	1.7052	3.0942	0.1581	0.2636	-0.1133	-0.0509	-0.3129	-0.0731	-0.2476	0.128	0.0236	0.0742	0.001	-0.0065	0.153	0.0458	0.0796	19.6696	5.1096	-5.5132
20	4.2214	-2.2152	-1.1999	2.8757	0.4133	2.4628	0.0706	0.1414	-0.1898	-0.2715	-0.1685	0.3431	-0.0496	0.1855	0.1071	0.1571	0.0176	-0.0182	0.147	0.0226	0.0794	17.6834	5.5568	-2.9675

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 57 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 58 through 74 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 75 through 88 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 89 through 100 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 101 through 117 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 118 through 128 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 129 through 156 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 11 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 12 through 23 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 24 through 33 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 34 through 44 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 45 through 59 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 60 through 88 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 89 through 100 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 101 through 117 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 118 through 128 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 129 through 140 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 141 through 156 )

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