PDB-5ghm: Crystal structure of human MTH1(G2K/D120N mutant) in complex with...

ID or keywords:

Entry

Database: PDB / ID: 5ghm

Title

Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 7.0

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: 1.5 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	Jun 20, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2017	Group: Database references
Revision 1.2	Mar 1, 2017	Group: Database references
Revision 1.3	Nov 7, 2018	Group: Data collection / Structure summary / Category: diffrn_source / struct / Item: _diffrn_source.pdbx_synchrotron_site / _struct.title
Revision 1.4	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ghm.cif.gz	163.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ghm.ent.gz	129.9 KB	Display	PDB format
PDBx/mmJSON format	5ghm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ghm_validation.pdf.gz	1003.8 KB	Display	wwPDB validaton report
Full document	5ghm_full_validation.pdf.gz	1007.4 KB	Display
Data in XML	5ghm_validation.xml.gz	19.5 KB	Display
Data in CIF	5ghm_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gh/5ghm ftp://data.pdbj.org/pub/pdb/validation_reports/gh/5ghm	HTTPS FTP

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Related structure data

Related structure data	5ghiC 5ghjC 5ghnC 5ghoC 5ghpC 5ghqC 5ws7C 6iliC C: citing same article (ref.)
Similar structure data	6ili-2 5ghj-1 5ghn-1 5hzx-1 6ehh-4 5ghj-2 5fso-d 5ghn-2 5ws7-2 6eq6-d 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

37.2 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
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)	45.790, 47.778, 123.610
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 / MutT homologue-1 / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked ...MutT homologue-1 / 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 / Fragment: UNP residues 42-197 / 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) / Strain (production host): BL21(DE3) 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: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 382 / 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: 1.87 Å³/Da / Density % sol: 34.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium citrate, Tris, NaCl

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Data collection

Diffraction	Mean temperature: 100 K
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: 1.5→50 Å / Num. obs: 44359 / % possible obs: 99.7 % / Redundancy: 6.9 % / R_merge(I) obs: 0.076 / Net I/σ(I): 47.4
Reflection shell	Resolution: 1.5→1.53 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.5→37.8 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.28

	R_factor	Num. reflection	% reflection
R_free	0.1961	2238	5.05 %
R_work	0.173	-	-
obs	0.1741	44286	99.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→37.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2542	0	65	382	2989

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2976
X-RAY DIFFRACTION	f_angle_d	0.927	4085
X-RAY DIFFRACTION	f_dihedral_angle_d	16.68	1134
X-RAY DIFFRACTION	f_chiral_restr	0.078	415
X-RAY DIFFRACTION	f_plane_restr	0.006	536

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 (%)
1.4978-1.5304	0.2624	130	0.2017	2523	X-RAY DIFFRACTION	97
1.5304-1.566	0.2372	148	0.1934	2577	X-RAY DIFFRACTION	100
1.566-1.6052	0.2198	133	0.191	2608	X-RAY DIFFRACTION	100
1.6052-1.6486	0.2322	155	0.1884	2594	X-RAY DIFFRACTION	100
1.6486-1.6971	0.2374	138	0.1948	2623	X-RAY DIFFRACTION	100
1.6971-1.7518	0.2316	145	0.1901	2586	X-RAY DIFFRACTION	100
1.7518-1.8145	0.2399	132	0.1895	2597	X-RAY DIFFRACTION	100
1.8145-1.8871	0.2109	136	0.1843	2631	X-RAY DIFFRACTION	100
1.8871-1.973	0.1878	149	0.1729	2585	X-RAY DIFFRACTION	100
1.973-2.077	0.2156	139	0.1736	2651	X-RAY DIFFRACTION	100
2.077-2.2071	0.2005	145	0.1754	2618	X-RAY DIFFRACTION	100
2.2071-2.3775	0.212	138	0.1742	2627	X-RAY DIFFRACTION	100
2.3775-2.6167	0.1978	136	0.1826	2643	X-RAY DIFFRACTION	100
2.6167-2.9952	0.2238	152	0.1859	2675	X-RAY DIFFRACTION	100
2.9952-3.7731	0.1517	129	0.1463	2717	X-RAY DIFFRACTION	100
3.7731-37.8122	0.1572	133	0.1593	2793	X-RAY DIFFRACTION	98

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	1.7274	-2.4622	0.9042	4.5445	-0.6351	1.0348	0.0724	0.0884	0.0279	0.0492	-0.2447	0.0449	-0.0362	0.0424	0.1336	0.13	-0.0193	0.0156	0.0901	0.0063	0.0687	2.9399	-3.8045	-15.6076
2	4.1161	0.3307	-0.2576	4.7859	0.388	5.1885	-0.2179	-0.0858	0.465	0.0947	0.2284	0.3962	-0.4852	-0.5244	0.0932	0.1305	0.0035	0.013	0.0952	0.031	0.1322	-5.9925	-18.3945	-16.4305
3	4.7055	-0.4422	-0.1821	2.015	0.4885	1.6485	0.1417	-0.2936	0.3593	0.9655	-0.0929	-0.1658	-0.0627	-0.115	0.0162	0.2744	-0.0347	-0.0094	0.0757	-0.0251	0.1278	1.8422	-4.6006	-6.9123
4	4.0965	2.9786	-2.318	3.542	-1.3858	4.8958	0.1169	-0.1822	0.0341	0.7834	-0.1206	0.4154	-0.6896	-0.1138	-0.0822	0.2743	-0.0001	0.0261	0.1124	0.0363	0.1759	1.0945	-10.9864	-5.0438
5	1.7154	-0.4229	0.3769	3.836	-2.206	2.201	0.1088	-0.1014	-0.0679	0.1836	-0.205	-0.1478	0.0446	0.0333	0.1232	0.1313	-0.0265	-0.008	0.095	-0.0038	0.0884	4.4466	-8.5039	-15.284
6	2.1713	-1.6425	-2.1496	7.0272	0.1322	3.4516	0.438	-0.7682	0.2226	0.18	-0.0822	0.2724	-0.2991	0.1062	-0.1351	0.247	-0.0138	0.0525	0.197	-0.012	0.1324	-4.7923	-20.3448	-5.9026
7	2.228	-1.5649	0.0395	6.056	0.4571	1.9266	-0.0339	-0.0212	0.0929	-0.034	0.0371	0.1237	-0.096	-0.2469	-0.028	0.0746	0.0105	0.0053	0.075	0.0105	0.0897	-5.4091	-21.5358	-19.5606
8	3.9966	-2.9929	1.5894	4.5307	-1.6817	2.8307	-0.0869	-0.0727	-0.0402	0.2436	0.0236	-0.0302	0.1803	0.059	0.0704	0.1275	-0.0065	0.0284	0.061	-0.01	0.0601	5.6316	-10.4065	-26.2446
9	4.6102	-0.0631	-2.3368	0.9995	0.2609	2.0748	-0.1298	0.3026	0.0625	-0.0099	0.0565	0.1368	0.0945	-0.2583	0.0581	0.0678	-0.0207	-0.0047	0.0902	0.001	0.083	13.6088	7.963	-14.7453
10	2.6991	-2.3738	-2.2754	5.9928	1.1078	4.9189	0.1655	-0.0328	-0.026	-0.1645	-0.1751	-0.0592	-0.1375	-0.0487	-0.0257	0.0371	-0.0202	0.0066	0.1153	0.0269	0.114	32.432	13.9577	-15.587
11	5.714	-0.876	1.2762	2.8797	-0.051	1.1334	0.3024	0.6126	0.4811	-0.1074	0.0102	0.2629	-0.4498	-1.0577	-0.2308	0.2036	0.0717	0.0567	0.3484	0.0635	0.1895	21.6793	22.0414	-14.2344
12	5.881	1.1772	0.1529	3.5992	0.6782	0.3005	-0.3638	1.3596	0.3669	-0.7201	0.3556	0.0627	0.3874	-0.6148	0.0541	0.2043	-0.1419	-0.0025	0.3907	0.0035	0.1122	18.9992	9.4553	-25.6882
13	1.6617	1.3439	-2.001	1.6247	-1.2683	3.7997	-0.3818	0.1878	-0.1993	-0.2825	0.1685	-0.1785	0.2682	0.0498	0.2079	0.1215	-0.0271	0.0008	0.1637	-0.0214	0.1204	20.9614	5.7404	-16.5172
14	7.2808	-3.8365	-2.5998	4.3206	1.3273	2.9219	-0.1071	0.0085	-0.0443	-0.1399	0.1708	0.004	-0.0647	-0.0068	-0.0278	0.0753	-0.0121	-0.0064	0.0972	-0.0053	0.0766	15.1756	8.4058	-13.6429
15	7.0307	-1.6005	-1.5743	5.3016	-0.4322	3.5176	-0.319	0.2758	-0.1832	-0.1691	0.6168	0.0616	-0.0323	-1.0334	0.0015	0.1822	0.0614	-0.003	0.3132	0.0632	0.0838	30.619	15.8711	-25.2435
16	5.6002	-1.275	-0.4477	2.4245	-0.0177	3.9675	0.1705	-0.0142	0.1212	-0.0247	-0.1689	0.0023	-0.2584	-0.0156	0.0138	0.0841	-0.0155	0.0078	0.0765	0.008	0.1048	31.1102	17.3782	-11.3256
17	4.9545	-1.255	-1.2332	4.2375	0.5434	2.7637	0.0546	0.0624	0.1468	0.0016	-0.0471	-0.2537	-0.2512	0.2203	-0.0032	0.0975	-0.0174	-0.0089	0.1101	0.0351	0.0742	20.9522	8.128	-5.2579
18	6.303	-3.6598	-2.3881	6.4023	3.3404	7.2489	-0.1214	0.219	-0.5874	-0.1201	-0.1072	0.439	0.3753	0.0479	0.226	0.1099	0.0106	0.0036	0.11	0.0346	0.1003	17.6531	2.0835	-3.0818

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 44 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 45 through 57 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 58 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 156 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 12 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 13 through 23 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 34 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 35 through 57 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 58 through 74 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 75 through 88 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 89 through 100 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 101 through 117 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 118 through 143 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 144 through 156 )

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