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

ID or keywords:

Entry

Database: PDB / ID: 6qqr

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: 1.56 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

-
Download

PDBx/mmCIF format	6qqr.cif.gz	182.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6qqr.ent.gz	143.8 KB	Display	PDB format
PDBx/mmJSON format	6qqr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6qqr_validation.pdf.gz	454.9 KB	Display	wwPDB validaton report
Full document	6qqr_full_validation.pdf.gz	455.1 KB	Display
Data in XML	6qqr_validation.xml.gz	19.6 KB	Display
Data in CIF	6qqr_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/6qqr ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qqr	HTTPS FTP

-
Related structure data

Related structure data	6qqqC 6qqtC 6qquC 6qqvC 6qqwC 6qqzC 6qr0C 6qr1C 6qr2C 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	6nvr-d 6qok-d 6qrb-d 6qo3-d 6qol-d 6qqu-d 6qrg-d 6qo6-d 6qov-d 6qr0-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

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

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

hetero molecules

53 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)	73.780, 78.711, 86.357
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-JDN / 1~{H}-indol-5-ylboronic acid Mass: 160.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₈BNO₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.13 %
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

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I02 / Wavelength: 0.9865 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9865 Å / Relative weight: 1

Reflection

Resolution: 1.56→86.36 Å / Num. obs: 72378 / % possible obs: 100 % / Redundancy: 7.7 % / B_iso Wilson estimate: 26.37 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.036 / R_pim(I) all: 0.014 / R_rim(I) all: 0.039 / Net I/σ(I): 26.3 / Num. measured all: 554554 / Scaling rejects: 4

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
1.56-1.64	7.8	0.781	10459	0.802	0.297	0.836	100
4.93-86.36	6.7	0.028	2475	0.997	0.012	0.031	99.3

-
Phasing

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

-
Processing

Software

Name	Version	Classification
Aimless	0.5.23	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: 1.56→58.173 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.31

	R_factor	Num. reflection	% reflection
R_free	0.203	3580	4.95 %
R_work	0.1812	-	-
obs	0.1822	72299	99.93 %

Solvent computation

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

Displacement parameters

B_iso max: 90.33 Å² / B_iso mean: 34.1924 Å² / B_iso min: 18.99 Å²

Refinement step

Cycle: final / Resolution: 1.56→58.173 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3223	0	12	294	3529
B_iso mean	-	-	32.15	45.17	-
Num. residues	-	-	-	-	427

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3337
X-RAY DIFFRACTION	f_angle_d	1.038	4575
X-RAY DIFFRACTION	f_chiral_restr	0.042	524
X-RAY DIFFRACTION	f_plane_restr	0.006	591
X-RAY DIFFRACTION	f_dihedral_angle_d	11.553	1203

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5589-1.5794	0.2589	128	0.248	2634	2762	100
1.5794-1.6011	0.2586	138	0.2415	2610	2748	100
1.6011-1.6239	0.2593	122	0.2291	2621	2743	100
1.6239-1.6482	0.2377	133	0.2177	2617	2750	100
1.6482-1.6739	0.2176	130	0.2053	2614	2744	100
1.6739-1.7014	0.2405	132	0.2027	2595	2727	100
1.7014-1.7307	0.2156	139	0.1936	2616	2755	100
1.7307-1.7622	0.1969	136	0.1904	2637	2773	100
1.7622-1.7961	0.2306	119	0.1879	2652	2771	100
1.7961-1.8327	0.2219	149	0.1886	2600	2749	100
1.8327-1.8726	0.1854	129	0.1839	2607	2736	100
1.8726-1.9162	0.2138	159	0.1789	2627	2786	100
1.9162-1.9641	0.2236	158	0.168	2590	2748	100
1.9641-2.0172	0.1827	139	0.1719	2621	2760	100
2.0172-2.0765	0.191	149	0.178	2614	2763	100
2.0765-2.1436	0.1968	131	0.1768	2645	2776	100
2.1436-2.2202	0.1925	144	0.1753	2613	2757	100
2.2202-2.3091	0.1907	137	0.1777	2655	2792	100
2.3091-2.4142	0.2012	141	0.1811	2637	2778	100
2.4142-2.5415	0.2463	155	0.1864	2648	2803	100
2.5415-2.7007	0.2297	148	0.1919	2648	2796	100
2.7007-2.9092	0.2278	127	0.1915	2679	2806	100
2.9092-3.202	0.2215	122	0.1921	2685	2807	100
3.202-3.6652	0.2214	128	0.1808	2699	2827	100
3.6652-4.6175	0.1645	143	0.1529	2729	2872	100
4.6175-58.2133	0.1807	144	0.1867	2826	2970	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	0.3336	-0.0288	-0.1598	0.126	-0.238	0.5557	-0.0088	-0.3224	0.1575	0.1107	-0.0423	-0.0733	-0.0815	-0.143	-0	0.2886	0.0265	0.0061	0.3344	-0.0178	0.2901	-32.1833	-13.3663	21.5506
2	-0.0048	-0.0173	0.002	0.0589	0.0378	0.0164	0.4354	-0.2569	0.3902	0.0093	0.1232	0.7113	-0.2159	-0.2755	0.0014	0.5731	0.0354	0.06	0.6218	-0.118	0.6521	-32.7393	-1.9992	31.0225
3	0.9568	-0.4186	0.1186	0.4895	-0.6039	0.6633	0.0775	-0.2288	0.0018	-0	0.014	0.2022	0.0515	-0.2595	0.0002	0.247	-0.0335	0.0206	0.3047	0.0272	0.2652	-40.3246	-20.0568	15.1638
4	0.7865	0.5448	0.3803	0.4063	-0.0597	1.1681	-0.0309	0.0614	-0.1035	0.171	0.0722	-0.0617	0.1219	-0.0473	0	0.2214	-0.0033	-0.0157	0.2515	-0.0036	0.268	-34.2021	-17.8451	6.346
5	0.2913	0.0078	0.1693	0.1092	-0.187	0.486	-0.0616	0.1654	0.1183	-0.0605	-0.0581	-0.0331	-0.1748	0.1897	0	0.2596	-0.0156	-0.0225	0.2251	-0.0309	0.2685	-19.646	-4.519	12.5776
6	0.5528	0.2644	0.3311	0.2503	-0.3194	1.2931	-0.0217	0.0147	0.0449	0.2002	0.0274	-0.1429	0.1705	0.1017	0.0002	0.2153	0.0344	-0.0157	0.2546	-0.0213	0.2662	-29.4008	-14.0663	11.0409
7	0.1478	-0.0272	0.1981	-0.0022	-0.0723	0.1715	-0.0509	0.1259	0.1192	0.0274	0.0001	-0.1293	-0.0572	-0.011	-0	0.2256	-0.0024	0.0104	0.2329	0.0169	0.2495	-31.1388	-9.3531	2.666
8	0.8597	-0.1507	0.0767	0.5762	-0.599	0.4251	-0.0361	-0.0584	-0.071	0.0718	0.0217	0.0449	0.0489	-0.0106	-0	0.232	0.0118	-0.0182	0.2352	-0.0316	0.2419	-20.8717	-12.6007	18.3516
9	0.7763	-0.4541	0.132	1.3933	-1.9057	3.417	-0.1715	-0.1302	0.4784	0.6052	-0.5503	0.1107	-0.2005	0.5541	-0.861	0.3499	-0.0328	0.048	0.0093	-0.2829	0.2751	-11.5573	-0.7225	25.0821
10	0.5265	0.2026	0.0078	0.2567	0.2138	0.253	0.1182	-0.0242	-0.0924	0.2869	-0.0022	-0.1601	0.0792	0.2156	-0.0001	0.3388	0.0339	-0.0448	0.2848	-0.0103	0.2856	2.8074	-4.3928	41.1875
11	0.6712	-0.4727	0.2422	0.3184	0.1098	0.1365	0.0075	0.1007	-0.1202	-0.041	0.0244	-0.2236	0.055	0.1234	0.0001	0.2748	-0.0337	0.0308	0.3092	-0.0266	0.253	3.0519	-1.972	24.1155
12	1.383	-0.4957	0.1329	1.2654	0.1829	0.938	-0.0288	-0.1611	-0.0417	0.0428	-0.1158	0.3678	0.149	-0.3005	-0.0001	0.2919	-0.0342	0.0185	0.2939	0.001	0.2128	-16.4828	-17.9762	35.8851
13	1.2277	0.4643	0.7607	0.9624	0.6111	1.1679	0.0783	-0.0625	-0.1012	0.1316	0.0386	-0.0832	0.0993	-0.0117	0.0001	0.267	0.0258	-0.0227	0.2083	-0.0069	0.2331	-5.9387	-19.517	30.4494
14	1.2992	0.0216	0.3318	0.7132	-0.8582	0.8756	0.0082	0	-0.0747	0.1011	0.0403	-0.1076	0.0232	0.0505	-0.0002	0.2197	-0.0009	0.0031	0.2163	-0.0197	0.2328	-15.7102	-19.8978	18.5676
15	0.8186	-0.0818	0.6417	0.8441	0.0213	-0.3167	-0.1079	0.3177	-0.2215	-0.261	0.1414	-0.1344	-0.083	0.0781	0.0001	0.257	-0.0375	0.0492	0.4092	-0.0884	0.2813	-22.5605	-19.5103	-4.622

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 17 )	A	0 - 17
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 29 )	A	18 - 29
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 30 through 48 )	A	30 - 48
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 83 )	A	49 - 83
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 100 )	A	84 - 100
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 101 through 115 )	A	101 - 115
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 116 through 131 )	A	116 - 131
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 132 through 155 )	A	132 - 155
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 156 through 182 )	A	156 - 182
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 183 through 203 )	A	183 - 203
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 204 through 227 )	A	204 - 227
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 62 )	B	0 - 62
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 63 through 131 )	B	63 - 131
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 132 through 181 )	B	132 - 181
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 182 through 231 )	B	182 - 231

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi