PDB-3q93: Crystal Structure of Human 8-oxo-dGTPase (MTH1)

ID or keywords:

Entry

Database: PDB / ID: 3q93

Title

Crystal Structure of Human 8-oxo-dGTPase (MTH1)

Components

7,8-dihydro-8-oxoguanine triphosphatase

Keywords

HYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / NUDIX / MutT-like / Magnesium Binding

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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. ...

Citation

Journal: To be Published
Title: Crystal Structure of Human 8-oxo-dGTPase (MTH1)
Authors: Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...

History

Deposition	Jan 7, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3q93.cif.gz	148 KB	Display	PDBx/mmCIF format
PDB format	pdb3q93.ent.gz	116.9 KB	Display	PDB format
PDBx/mmJSON format	3q93.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q9/3q93 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/3q93	HTTPS FTP

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Related structure data

Related structure data	1iryS S: Starting model for refinement
Similar structure data	3zr0-1 5otm-1 6jvm-1 6jvh-1 5ngr-1 6jvq-1 5mze-4 6f1x-1 5anu-d 6jvo-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

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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) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

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

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

hetero molecules

41 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 software
20.7 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 software
20.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.544, 67.681, 82.678
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 / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1 Mass: 20142.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTH1, NUDT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE References: UniProt: P36639, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.07 Å³/Da / Density % sol: 40.51 %
Crystal grow	Temperature: 277 K / pH: 7.4 Details: 0.26 M AMMONIUM SULFATE, 22 % w/v PEG4000, 13 % GLYCEROL, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 16, 2010 / Details: MIRRORS
Radiation	Monochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.8→33.96 Å / Num. obs: 31366 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / B_iso Wilson estimate: 24.2 Å² / R_merge(I) obs: 0.108 / R_sym value: 0.108 / Net I/σ(I): 4.4
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.701 / Mean I/σ(I) obs: 2.3 / R_sym value: 0.701 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IRY

1iry

Resolution: 1.8→33.96 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.233	1587	5.07 %
R_work	0.201	-	-
obs	0.203	31318	99 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.08 Å² / k_sol: 0.39 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.6957 Å²	-0 Å²	0 Å²
2-	-	-5.906 Å²	-0 Å²
3-	-	-	13.6017 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→33.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2508	0	42	215	2765

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2640
X-RAY DIFFRACTION	f_angle_d	1.066	3574
X-RAY DIFFRACTION	f_dihedral_angle_d	12.921	981
X-RAY DIFFRACTION	f_chiral_restr	0.066	368
X-RAY DIFFRACTION	f_plane_restr	0.005	463

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 (%)
1.8-1.8643	0.3617	146	0.3088	2890	X-RAY DIFFRACTION	98
1.8643-1.939	0.3163	150	0.2642	2916	X-RAY DIFFRACTION	99
1.939-2.0272	0.2973	166	0.2363	2911	X-RAY DIFFRACTION	99
2.0272-2.1341	0.2421	142	0.2137	2947	X-RAY DIFFRACTION	98
2.1341-2.2677	0.2339	153	0.2043	2963	X-RAY DIFFRACTION	99
2.2677-2.4428	0.2429	168	0.2087	2944	X-RAY DIFFRACTION	99
2.4428-2.6885	0.245	145	0.2055	2983	X-RAY DIFFRACTION	99
2.6885-3.0774	0.2832	170	0.2037	2997	X-RAY DIFFRACTION	99
3.0774-3.8763	0.241	175	0.1829	3000	X-RAY DIFFRACTION	100
3.8763-33.9636	0.1678	172	0.1815	3180	X-RAY DIFFRACTION	100

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	3.7016	0.7783	-0.4605	8.6255	-4.9026	3.9524	0.2581	0.0502	-0.5524	0.0249	-0.323	0.1577	0.0432	0.2671	-0.0615	0.1763	-0.0033	-0.0075	0.1893	0.0015	0.1797	-4.158	5.6408	11.9594
2	3.9136	-0.0583	-2.6008	5.1968	-1.9739	9.2121	0.0131	0.1932	0.0513	0.2385	0.1389	0.1313	-0.0525	-0.4483	-0.0764	0.175	-0.0009	0.0364	0.1411	0.0004	0.0868	-0.0908	19.0664	14.1031
3	5.8155	3.3846	0.6012	2.8188	0.6024	0.1125	0.1893	0.2974	0.0913	0.1316	-0.2415	0.3838	0.0427	-0.1854	0.0127	0.1785	-0.0056	0.0044	0.2288	-0.0018	0.209	-11.2724	8.3532	9.1532
4	7.3668	-6.169	-0.0486	7.3702	1.0445	4.214	0.2991	0.6619	-0.1162	-0.4341	-0.4063	0.5825	0.0368	-0.068	0.1161	0.1486	-0.0479	-0.0119	0.1931	-0.0015	0.2123	-6.3613	12.7979	3.9887
5	2.987	-1.1221	3.1107	5.5784	-6.9091	9.8949	0.0997	-0.1949	-0.4119	0.2082	0.0678	0.1988	-0.0606	-0.3087	-0.0831	0.1839	-0.0115	0.0183	0.1648	-0.0112	0.1258	0.4462	0.9117	16.7453
6	3.5251	0.0801	0.9997	3.9035	0.7567	0.352	0.0512	0.1643	0.5067	-0.2133	-0.0111	0.5206	-0.1368	-0.1851	-0.1053	0.2314	0.0276	0.032	0.1738	0.0678	0.2487	-3.9612	22.4704	9.3621
7	3.3775	-0.2969	-0.6771	5.4206	0.4499	2.8377	0.0139	0.136	0.2139	0.0414	-0.0515	-0.3274	-0.1028	0.0282	0.0378	0.1345	-0.0162	-0.0025	0.1345	0.01	0.1383	9.4445	14.3967	10.8005
8	6.1839	-0.6854	2.6957	4.2219	-1.6483	2.3117	0.1242	0.1941	-0.4402	0.0288	-0.0971	-0.081	0.426	0.3151	-0.0816	0.1416	0.0065	0.0118	0.1079	-0.0278	0.1119	9.0137	2.2244	12.9706
9	5.6885	-0.4083	-2.7385	9.0313	5.8414	4.8305	0.269	-0.0297	-0.9371	0.681	-0.7253	0.4696	0.45	-0.3171	0.3212	0.1658	-0.0203	-0.0928	0.2667	-0.1453	0.542	33.5606	-6.6848	10.6896
10	2.1351	0.9167	-3.0635	1.8034	-0.4138	3.3439	-0.2834	1.6646	-4.2141	0.0966	-0.3102	-0.7936	0.1356	-0.5197	0.1933	0.1409	0.057	-0.21	0.2155	-0.3101	1.7255	28.6552	-19.4117	7.2631
11	2.6141	-1.6006	-0.8476	4.2747	0.5792	0.5401	0.3185	0.7461	-1.8328	0.2303	-0.186	-0.1099	-0.1536	-0.0195	0.0483	0.1644	0.0252	-0.1141	0.3097	-0.2397	0.8203	38.4266	-8.6994	6.8769
12	4.9523	-1.9667	-3.3827	4.7491	-0.1051	3.1447	0.0628	1.9546	-2.3411	-0.1338	-0.5313	-0.5047	-0.064	-0.3909	0.0734	0.0725	0.0701	-0.0939	0.609	-0.5843	0.9127	35.2976	-10.6147	0.6893
13	9.5561	-0.325	-6.9808	0.8228	0.6446	8.5793	0.2328	-0.3652	-1.1243	0.1716	-0.3414	-0.486	-0.343	0.7718	0.0934	0.2052	-0.0505	-0.1234	0.2003	0.0342	0.351	29.9101	-4.7564	15.747
14	9.7689	-0.7258	-0.9836	5.5502	1.0638	2.8929	0.0184	1.6764	-4.5899	0.101	-0.7373	0.0111	0.9507	-0.8651	0.5895	0.0862	0.0934	0.0711	0.5193	-0.7744	1.9862	32.7074	-21.3978	0.7551
15	7.9516	0.7541	-0.3755	1.3929	0.2653	1.3313	0.1581	0.8587	-2.3739	0.0428	-0.1924	-0.1191	0.2252	-0.0511	-0.0484	0.2136	0.0307	-0.0973	0.2945	-0.3196	1.0479	19.1632	-14.148	7.9517
16	9.1717	-0.1602	-1.2959	3.8197	-3.8918	6.9802	0.2857	0.0036	-0.5784	0.2096	-0.2258	-0.1671	-0.2195	-0.0207	-0.1244	0.2083	-0.0005	-0.0632	0.1657	-0.0333	0.2505	20.7949	-3.3506	14.4558

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 3:12)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 13:33)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 34:54)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 55:69)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 70:86)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 87:108)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 109:131)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 132:156)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 3:12)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 13:31)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 32:51)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 52:69)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 70:88)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 89:107)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 108:130)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 131:156)

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