PDB-6qr2: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from...

ID or keywords:

Entry

Database: PDB / ID: 6qr2

Title

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor

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 modification / methylation / cytoplasm
Similarity search - Function

Biological species

Mycobacterium abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 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: J.Med.Chem. / Year: 2019
Title: Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Authors: Whitehouse, A.J. / Thomas, S.E. / Brown, K.P. / Fanourakis, A. / Chan, D.S. / Libardo, M.D.J. / Mendes, V. / Boshoff, H.I.M. / Floto, R.A. / Abell, C. / Blundell, T.L. / Coyne, A.G.

History

Deposition	Feb 19, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	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	6qr2.cif.gz	182.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6qr2.ent.gz	143.6 KB	Display	PDB format
PDBx/mmJSON format	6qr2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6qr2_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6qr2_full_validation.pdf.gz	1 MB	Display
Data in XML	6qr2_validation.xml.gz	20.4 KB	Display
Data in CIF	6qr2_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/6qr2 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/6qr2	HTTPS FTP

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Related structure data

Related structure data	6qqqC 6qqrC 6qqtC 6qquC 6qqvC 6qqwC 6qqzC 6qr0C 6qr1C 6qr3C 6qr4C 6qr7C 6qr9C 6qraC 6qrbC 6qrcC 6qrdC 6qreC 6qrfC 6qrgC 6nvrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qrd-d 6qrc-d 6qqx-d 6qr3-d 6qr8-d 6nw7-d 6qoq-d 6qrb-d 6qr1-d 6qrf-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

53.8 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)	74.881, 76.728, 86.588
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-JQB / 5-azanyl-3-[1-[(2-oxidanylpyridin-3-yl)methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile Mass: 330.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₄N₆O
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.35 Å³/Da / Density % sol: 47.71 %
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: I03 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 1.55→86.59 Å / Num. obs: 73287 / % possible obs: 99.4 % / Redundancy: 7.9 % / B_iso Wilson estimate: 26.83 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.042 / R_pim(I) all: 0.016 / R_rim(I) all: 0.045 / Net I/σ(I): 22.1 / Num. measured all: 578145

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
1.55-1.63	8	0.723	10650	0.838	0.27	0.772	100
4.89-86.59	7.2	0.033	2552	0.999	0.013	0.036	99.9

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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
PHENIX	1.9_1692	refinement
Aimless	0.5.31	data scaling
PHASER	2.5.7	phasing
PDB_EXTRACT	3.24	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr

Resolution: 1.55→38.364 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.75

	R_factor	Num. reflection	% reflection
R_free	0.1821	3793	5.18 %
R_work	0.1687	-	-
obs	0.1694	73205	99.36 %

Solvent computation

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

Displacement parameters

B_iso max: 120.99 Å² / B_iso mean: 34.3639 Å² / B_iso min: 19 Å²

Refinement step

Cycle: final / Resolution: 1.55→38.364 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3135	0	65	300	3500
B_iso mean	-	-	40.27	46.31	-
Num. residues	-	-	-	-	413

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3324
X-RAY DIFFRACTION	f_angle_d	1.045	4564
X-RAY DIFFRACTION	f_chiral_restr	0.041	511
X-RAY DIFFRACTION	f_plane_restr	0.006	584
X-RAY DIFFRACTION	f_dihedral_angle_d	11.393	1188

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5451-1.5647	0.2917	133	0.2483	2566	2699	100
1.5647-1.5853	0.2342	146	0.2354	2531	2677	100
1.5853-1.607	0.2577	142	0.2158	2569	2711	100
1.607-1.6299	0.2084	113	0.2092	2595	2708	100
1.6299-1.6543	0.2255	142	0.2018	2523	2665	100
1.6543-1.6801	0.2377	125	0.1975	2587	2712	100
1.6801-1.7077	0.2131	147	0.1877	2558	2705	100
1.7077-1.7371	0.2098	124	0.1833	2570	2694	100
1.7371-1.7687	0.1919	127	0.1749	2559	2686	100
1.7687-1.8027	0.1773	123	0.1751	2589	2712	100
1.8027-1.8395	0.1905	134	0.1688	2569	2703	100
1.8395-1.8795	0.1916	162	0.1743	2550	2712	100
1.8795-1.9232	0.2012	174	0.1707	2534	2708	100
1.9232-1.9713	0.2026	179	0.1732	2554	2733	100
1.9713-2.0246	0.2015	171	0.1688	2527	2698	100
2.0246-2.0842	0.2118	122	0.1706	2147	2269	83
2.0842-2.1515	0.1806	149	0.1727	2559	2708	100
2.1515-2.2283	0.2026	131	0.1704	2588	2719	100
2.2283-2.3176	0.2005	126	0.1713	2587	2713	100
2.3176-2.423	0.1944	139	0.171	2610	2749	100
2.423-2.5507	0.1889	139	0.1728	2618	2757	100
2.5507-2.7105	0.1861	143	0.1762	2585	2728	100
2.7105-2.9197	0.2159	140	0.18	2593	2733	100
2.9197-3.2134	0.1884	120	0.1769	2660	2780	100
3.2134-3.6781	0.168	145	0.1597	2626	2771	100
3.6781-4.6327	0.1414	133	0.1426	2685	2818	100
4.6327-38.3758	0.1718	164	0.169	2773	2937	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	1.8596	-0.8891	-0.7509	3.096	0.1362	2.6162	0.0806	0.5691	-0.1541	-0.7568	-0.1678	-0.1091	0.1732	-0.0537	0.0529	0.3208	-0.0041	-0.0032	0.3134	0.01	0.2312	-32.1193	13.1037	-22.4646
2	2.2542	-1.0659	-0.8814	3.6408	2.0611	2.7602	0.0487	0.2915	-0.2108	-0.38	-0.0595	0.3397	-0.1264	-0.2308	0.0445	0.2728	0.0061	-0.0367	0.3176	0.0288	0.2767	-38.9453	14.5435	-19.5947
3	0.912	-0.6682	-0.3496	1.3527	0.593	1.8828	0.0164	-0.0524	0.1049	-0.0551	0.04	0.0718	-0.1468	-0.0679	-0.0465	0.2032	0.003	0.0113	0.252	0.0076	0.2551	-34.8971	17.0321	-6.2975
4	2.0505	0.7249	0.4327	1.1413	1.0769	2.7174	-0.0461	0.0515	-0.2894	0.2018	0.024	0.0939	0.4455	0.1787	-0.0038	0.2648	0.008	0.0137	0.2401	-0.0244	0.2539	-20.2087	4.1978	-12.9005
5	1.8625	-0.1287	-0.5555	0.1607	0.1556	1.0394	-0.0202	0.0616	0.0789	-0.0321	0.064	-0.0089	0.0333	-0.0258	-0.0379	0.2244	-0.0185	-0	0.218	-0.0038	0.2325	-27.1727	11.7753	-11.6489
6	7.0973	2.1232	-0.3311	0.9732	0.0374	0.0824	0.5105	0.3611	-0.7626	-0.0765	-0.3509	0.2556	0.5025	-0.2465	-0.0656	0.404	-0.0377	-0.068	0.3691	-0.0791	0.3666	-16.3624	0.7009	-25.5662
7	1.0757	-0.5543	0.2501	1.9955	-0.2311	0.9473	0.0575	0.0954	0.174	-0.4408	0.0534	-0.3195	-0.1312	0.1934	-0.1016	0.3067	-0.0521	0.0436	0.275	-0.0214	0.2623	2.2233	5.1218	-40.9166
8	0.9864	-0.4183	-0.6347	3.2501	2.684	2.4348	-0.0357	-0.1483	0.1517	0.3181	0.1912	-0.1712	0.3112	0.2618	-0.1414	0.2869	0.0314	-0.0427	0.3308	-0.0258	0.2585	2.5541	2.4444	-24.3259
9	3.2613	0.806	0.0505	3.4905	-0.1944	2.3023	0.0278	0.3182	0.3441	-0.204	0.0038	0.4332	-0.3595	-0.3364	-0.0009	0.3316	-0.0019	-0.0481	0.332	0.0559	0.3194	-18.6876	22.7228	-34.2633
10	0.8445	-0.66	-0.5479	1.1825	0.8434	1.515	0.0049	0.1372	0.0795	-0.298	0.0346	-0.0036	-0.2503	0.0617	-0.0328	0.2631	-0.0501	0.013	0.2182	0.0069	0.2145	-7.5786	16.4375	-32.0652
11	1.2749	-0.7731	-0.4804	0.9345	0.7523	1.8169	0.001	0.0829	0.0767	-0.2137	0.0844	-0.1737	-0.155	0.0717	-0.0919	0.3048	-0.0674	0.0286	0.2483	0.0096	0.2503	-5.4226	18.1432	-32.5898
12	1.3623	0.3467	0.0559	1.8087	-0.0905	1.1205	0.0091	0.0795	0.1957	-0.1285	-0.0228	0.1458	-0.0442	-0.0862	0.0057	0.223	-0.0119	0.0045	0.2411	-0.0025	0.2556	-16.1314	17.2685	-22.0401
13	1.0531	1.4267	-1.8611	1.9299	-2.5202	3.2979	-0.1519	-0.0868	0.3989	0.3121	0.0326	-0.3467	-0.6304	0.1137	-0.0501	0.3099	-0.0322	-0.0358	0.3362	0.0209	0.4556	-16.5513	25.3837	-7.2265
14	3.1393	0.2894	0.0685	1.5004	-0.2884	1.5933	0.0471	-0.5457	0.4069	0.2335	-0.0319	0.1358	0.2027	0.0058	-0.0012	0.2805	0.0131	0.0386	0.325	-0.0671	0.2928	-33.6978	22.023	6.6941
15	1.1805	-0.8309	-1.3586	1.8466	2.0592	2.7074	-0.1259	-0.6494	0.4325	0.5317	0.155	-0.1826	0.1192	0.0126	0.0022	0.287	0.0252	-0.0582	0.593	-0.1097	0.3685	-18.3084	19.3592	6.2402
16	5.0778	-1.2133	1.1337	4.1182	-0.1366	5.1966	0.2694	0.5749	-0.6047	-0.0068	-0.0249	-0.4457	0.537	-0.2525	-0.163	0.2554	-0.0326	-0.0378	0.3391	-0.0385	0.3973	-8.1615	9.4428	-1.9796

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 0 through 19 )	A	0 - 19
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 48 )	A	20 - 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 180 )	A	156 - 180
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 181 through 203 )	A	181 - 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 40 )	B	0 - 40
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 41 through 100 )	B	41 - 100
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 101 through 131 )	B	101 - 131
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 132 through 155 )	B	132 - 155
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 156 through 182 )	B	156 - 182
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 183 through 203 )	B	183 - 203
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 204 through 222 )	B	204 - 222
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 223 through 232 )	B	223 - 232

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