PDB-6nw7: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from...

ID or keywords:

Entry

Database: PDB / ID: 6nw7

Title

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with S-Adenosyl-L-homocysteine

Components

tRNA (guanine-N(1)-)-methyltransferase

Keywords

TRANSFERASE / TrmD / tRNA methyltransferase / SPOUT methyltransferase

Function / homology

Function and homology information

tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / cytosol
Similarity search - Function

Biological species

Mycobacterium abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.481 Å

Authors

Thomas, S.E. / Whitehouse, A.J. / Coyne, A.G. / Abell, C. / Mendes, V. / Blundell, T.L.

Funding support

United Kingdom, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2020
Title: Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.
Authors: Thomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. / Boshoff, H.I.M. / Jackson, M. / Abell, ...

History

Deposition	Feb 6, 2019	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 26, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2024	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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Download

PDBx/mmCIF format	6nw7.cif.gz	187.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6nw7.ent.gz	147.5 KB	Display	PDB format
PDBx/mmJSON format	6nw7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6nw7_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6nw7_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6nw7_validation.xml.gz	20.9 KB	Display
Data in CIF	6nw7_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nw/6nw7 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nw7	HTTPS FTP

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Related structure data

Related structure data	6nvrSC 6nw6C 6qo2C 6qo3C 6qo4C 6qo6C 6qoaC 6qocC 6qodC 6qoeC 6qofC 6qogC 6qohC 6qoiC 6qojC 6qokC 6qolC 6qomC 6qonC 6qooC 6qopC 6qoqC 6qorC 6qosC 6qotC 6qouC 6qovC 6qowC 6qoxC 6qqsC 6qqxC 6qqyC 6qr5C 6qr6C 6qr8C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qox-d 6qou-d 6qog-d 6qok-d 6qo4-d 6qqx-d 6qot-d 6qow-d 6qr1-d 6qr4-d 6nw6-d 6nvr-d 6qqy-d 6qrc-d 6qr8-d 6qqu-d 6qor-d 6qqz-d 6qrb-d 6qr9-d 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

Deposited unit

A: tRNA (guanine-N(1)-)-methyltransferase

B: tRNA (guanine-N(1)-)-methyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	75.334, 78.254, 88.005
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase Mass: 26434.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: trmD, MAB_3226c / Production host: Escherichia coli (E. coli) References: UniProt: B1MDI3, tRNA (guanine37-N1)-methyltransferase
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 314 / 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: 49.86 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.08M Sodium cacodylate pH 6.5 -7.0, 1-2 M Ammonium sulphate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9282 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9282 Å / Relative weight: 1

Reflection

Resolution: 1.48→88 Å / Num. obs: 87094 / % possible obs: 99.9 % / Redundancy: 7.7 % / B_iso Wilson estimate: 22.68 Å² / CC_1/2: 1 / R_merge(I) obs: 0.032 / R_pim(I) all: 0.012 / R_rim(I) all: 0.035 / Net I/σ(I): 28.6 / Num. measured all: 672548

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.48-1.56	7.7	0.72	12561	0.826	0.275	0.772	99.9
4.68-88	7	0.022	2974	0.999	0.008	0.023	99.4

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Phasing

Phasing	Method: molecular replacement
Phasing MR	Model details: Phaser MODE: MR_AUTO

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Processing

Software

Name	Version	Classification
Aimless	0.5.15	data scaling
PHASER	2.5.7	phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.24	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr

Resolution: 1.481→58.479 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.08

	R_factor	Num. reflection	% reflection
R_free	0.1945	4233	4.86 %
R_work	0.1783	-	-
obs	0.1791	87010	99.91 %

Solvent computation

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

Displacement parameters

B_iso max: 102.86 Å² / B_iso mean: 31.5919 Å² / B_iso min: 15.84 Å²

Refinement step

Cycle: final / Resolution: 1.481→58.479 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3252	0	57	314	3623
B_iso mean	-	-	32.97	41.78	-
Num. residues	-	-	-	-	429

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3439
X-RAY DIFFRACTION	f_angle_d	1.089	4718
X-RAY DIFFRACTION	f_chiral_restr	0.051	535
X-RAY DIFFRACTION	f_plane_restr	0.006	608
X-RAY DIFFRACTION	f_dihedral_angle_d	14.252	1261

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4809-1.4977	0.2563	138	0.2615	2724	2862	100
1.4977-1.5154	0.2666	137	0.2397	2734	2871	100
1.5154-1.5338	0.2465	137	0.2249	2749	2886	100
1.5338-1.5533	0.2322	153	0.2185	2683	2836	100
1.5533-1.5737	0.2323	144	0.2169	2747	2891	100
1.5737-1.5953	0.2404	128	0.2057	2746	2874	100
1.5953-1.618	0.2265	158	0.2008	2691	2849	100
1.618-1.6422	0.2132	131	0.1952	2738	2869	100
1.6422-1.6679	0.1979	134	0.1926	2752	2886	100
1.6679-1.6952	0.2042	144	0.1913	2724	2868	100
1.6952-1.7244	0.2008	137	0.1874	2745	2882	100
1.7244-1.7558	0.1873	134	0.1852	2754	2888	100
1.7558-1.7896	0.1838	140	0.1845	2729	2869	100
1.7896-1.8261	0.1964	140	0.1872	2718	2858	100
1.8261-1.8658	0.2005	130	0.1801	2778	2908	100
1.8658-1.9092	0.1996	145	0.1781	2737	2882	100
1.9092-1.957	0.1768	161	0.1728	2716	2877	100
1.957-2.0099	0.1765	145	0.1653	2746	2891	100
2.0099-2.069	0.191	148	0.1781	2741	2889	100
2.069-2.1358	0.2263	134	0.1787	2755	2889	100
2.1358-2.2121	0.2146	128	0.175	2779	2907	100
2.2121-2.3007	0.1814	158	0.1704	2744	2902	100
2.3007-2.4054	0.1837	128	0.1794	2784	2912	100
2.4054-2.5323	0.1919	128	0.1754	2791	2919	100
2.5323-2.6909	0.187	160	0.1834	2767	2927	100
2.6909-2.8987	0.212	107	0.1916	2823	2930	100
2.8987-3.1904	0.2213	157	0.1933	2767	2924	100
3.1904-3.6519	0.211	138	0.1743	2813	2951	100
3.6519-4.6008	0.1578	150	0.1546	2861	3011	100
4.6008-58.5244	0.1902	161	0.1742	2941	3102	99

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	0.1362	-0.1303	0.1814	0.0833	-0.1764	0.2693	-0.0504	-0.2624	0.037	0.3414	0.0195	0.2136	-0.2069	-0.1986	-0.0002	0.298	0.0102	0.0161	0.2667	0.0107	0.2054	-32.9222	-12.9599	22.7336
2	0.6094	-0.2233	0.0847	0.2472	-0.2642	0.2499	0.0053	-0.1508	0.0344	0.1949	0.029	0.2134	-0.0077	-0.2704	0.0001	0.2656	0.0132	0.0465	0.2607	0.0122	0.2245	-38.9682	-14.3382	20.182
3	0.5087	0.138	0.35	0.0349	0.1904	1.0014	0.0322	0.0362	-0.1051	0.0856	0.0926	-0.0264	0.0904	-0.0216	0.0002	0.1725	-0.0051	-0.0034	0.2016	-0.0092	0.2231	-35.112	-17.316	6.4766
4	0.3149	0.035	0.0199	0.0036	-0.0559	0.2201	-0.0775	0.0741	0.0908	-0.1161	0.0014	0.0193	-0.2731	0.2209	-0	0.2294	-0.012	-0.0076	0.2092	-0.0265	0.2206	-20.2687	-4.2161	12.9326
5	0.9836	0.0684	0.1155	0.2388	0.1758	0.1822	0.0068	0.0123	-0.0399	0.0201	0.0353	-0.0184	-0.0246	0.0061	0	0.1942	0.0128	0	0.1845	-0.01	0.1921	-27.3202	-11.8745	11.7883
6	0.195	-0.1674	-0.0411	0.4288	-0.2479	0.902	0.1198	-0.2218	0.1796	0.2142	-0.3861	0.1874	-0.0604	0.1573	-0.4993	0.5123	0.0205	0.2162	0.2996	-0.3334	0.2201	-19.852	0.6689	27.1895
7	0.4047	0.3863	0.0658	0.3341	0.084	0.0405	0.0491	-0.0297	-0.1575	0.2445	0.0922	-0.1559	0.0629	0.1584	0.0001	0.2723	0.0437	-0.037	0.2361	-0.0169	0.2246	1.8182	-4.9148	40.0682
8	0.36	-0.2815	0.3681	0.1644	0.1232	0.1511	-0.05	0.1306	-0.0568	-0.0435	0.1834	-0.1775	-0.0609	0.3091	0.0001	0.2267	-0.0469	0.0381	0.3046	-0.0391	0.2112	2.8499	-2.233	24.5687
9	0.3304	-0.2209	-0.1616	0.367	-0.1737	0.248	0.1284	0.0798	-0.4006	-0.1186	-0.0892	0.505	0.3601	-0.3833	0.0011	0.3148	-0.0265	-0.0363	0.3167	-0.0041	0.3619	-20.7193	-24.0908	30.381
10	0.5444	-0.238	0.0135	0.1263	-0.0408	0.015	0.2712	-0.4031	-0.2303	0.4781	-0.2798	0.5096	0.1355	-0.4978	0.0327	0.4234	-0.0358	0.1199	0.3503	0.0317	0.2046	-16.191	-18.4961	43.318
11	0.6199	0.4934	0.395	0.6318	0.5604	0.838	0.0096	-0.0658	-0.092	0.1686	0.0279	-0.0411	0.1086	0.0664	0	0.2407	0.0407	-0.0166	0.1934	-0.0027	0.2078	-6.3943	-17.4197	32.2488
12	0.4104	0.1393	0.0865	0.1607	-0.2201	0.3404	0.0147	-0.0604	-0.1044	0.0884	-0.0323	-0.0313	-0.0032	-0.063	-0	0.1809	0.0034	0.0111	0.1861	-0.0089	0.2417	-16.3183	-19.6537	18.1376
13	0.5421	-0.0794	0.5508	0.7631	0.2767	0.3153	-0.0273	0.4246	-0.3288	-0.2658	0.144	-0.1017	-0.1045	0.224	0.0005	0.2284	-0.0312	0.0367	0.3744	-0.0952	0.2647	-26.2451	-21.3916	-6.258
14	0.1033	0.0298	0.0798	0.0286	-0.0091	0.0314	0.0813	-0.2826	0.5488	0.0538	0.1139	-0.3356	-0.2219	-0.2941	0	0.2376	0.0309	0.0596	0.2806	-0.0624	0.3585	-8.3713	-8.9514	1.8083

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 18 )	A	-1 - 18
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 48 )	A	19 - 48
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 83 )	A	49 - 83
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 100 )	A	84 - 100
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 101 through 155 )	A	101 - 155
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 156 through 178 )	A	156 - 178
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 179 through 203 )	A	179 - 203
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 204 through 227 )	A	204 - 227
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 0 through 29 )	B	0 - 29
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 48 )	B	30 - 48
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 49 through 131 )	B	49 - 131
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 132 through 182 )	B	132 - 182
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 183 through 222 )	B	183 - 222
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 223 through 233 )	B	223 - 233

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