PDB-6w14: Crystal structure of tRNA (guanine-N(1)-)-methyltransferase from ...

ID or keywords:

Entry

Database: PDB / ID: 6w14

Title

Crystal structure of tRNA (guanine-N(1)-)-methyltransferase from Mycobacterium smegmatis

Components

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

Keywords

TRANSFERASE / SSGCID / tRNA (guanine-N(1)-)-methyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

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

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of tRNA (guanine-N(1)-)-methyltransferase from Mycobacterium smegmatis
Authors: Dranow, D.M. / Bolejack, M.J. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Mar 3, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	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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PDBx/mmCIF format	6w14.cif.gz	113.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w1/6w14 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w14	HTTPS FTP

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Related structure data

Related structure data	5zhiS S: Starting model for refinement
Similar structure data	6qoo-d 5a6c-2 6qqv-d 3v2h-3 6uev-1 6qop-d 3sib-1 5gqt-d 3hft-1 6t87-d 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

Deposited unit

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

26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

defined by author&software
Evidence: gel filtration
52.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.460, 58.460, 114.440
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2
Space group name Hall	P4nw2abw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase Mass: 26057.330 Da / Num. of mol.: 1 / Fragment: MysmA.00937.a.AE1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: trmD, MSMEI_2377 / Plasmid: MysmA.00937.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: I7FBD0, UniProt: A0QV40*PLUS, tRNA (guanine37-N1)-methyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase

Mass: 26057.330 Da / Num. of mol.: 1 / Fragment: MysmA.00937.a.AE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: trmD, MSMEI_2377 / Plasmid: MysmA.00937.a.AE1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I7FBD0, UniProt: A0QV40*PLUS, tRNA (guanine37-N1)-methyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.88 Å³/Da / Density % sol: 34.44 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MysmA.00937.a.AE1.PW38670 at 19.05 mg/ml mixed 1:1 with MCSG1(d3): 30% (v/v) PEG-400, 0.1 M Tris-HCl. pH = 8.5, 0.2 M MgCl2. Tray: 311556d3. Puck: wdc6-11.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 4, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 13969 / % possible obs: 99.2 % / Redundancy: 12.771 % / B_iso Wilson estimate: 44.124 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.075 / R_rim(I) all: 0.078 / Χ²: 0.965 / Net I/σ(I): 18.41

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	7.06	0.617	2.8	1018	0.971	0.668	99.7
2.05-2.11	9.287	0.466	4.26	998	0.964	0.494	99.9
2.11-2.17	12.724	0.466	5.55	959	0.977	0.486	100
2.17-2.24	13.856	0.351	7.54	923	0.993	0.365	99.2
2.24-2.31	13.816	0.312	8.21	896	0.993	0.324	98.5
2.31-2.39	13.859	0.246	9.85	864	0.996	0.256	98.7
2.39-2.48	13.805	0.196	12.02	837	0.999	0.203	97.8
2.48-2.58	13.845	0.183	13.01	815	0.997	0.19	99.3
2.58-2.7	13.969	0.157	14.97	771	0.997	0.163	98.6
2.7-2.83	13.895	0.13	17.14	762	0.997	0.135	98.8
2.83-2.98	13.846	0.097	21.5	707	0.998	0.101	98.6
2.98-3.16	13.92	0.084	26	684	0.999	0.087	99.6
3.16-3.38	13.819	0.072	30.02	663	0.999	0.075	99.7
3.38-3.65	13.646	0.063	36.43	605	0.999	0.065	99.5
3.65-4	13.425	0.057	39.91	558	0.999	0.059	99.6
4-4.47	13.103	0.058	40.97	522	0.999	0.06	99.4
4.47-5.16	13.028	0.053	42.61	465	0.999	0.055	99.8
5.16-6.32	12.952	0.054	41.86	395	0.998	0.056	99.7
6.32-8.94	12.387	0.054	41.48	323	0.998	0.056	100
8.94-50	10.657	0.054	40.65	204	0.998	0.056	99

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.17.1-3660	refinement
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ZHI

5zhi

Resolution: 2→40.89 Å / SU ML: 0.2539 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2146

	R_factor	Num. reflection	% reflection
R_free	0.2793	1406	10.09 %
R_work	0.2114	-	-
obs	0.2181	13934	99 %

Solvent computation

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

Displacement parameters

B_iso mean: 48.79 Å²

Refinement step

Cycle: LAST / Resolution: 2→40.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1549	0	0	53	1602

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	1584
X-RAY DIFFRACTION	f_angle_d	0.7877	2162
X-RAY DIFFRACTION	f_chiral_restr	0.0505	244
X-RAY DIFFRACTION	f_plane_restr	0.0055	284
X-RAY DIFFRACTION	f_dihedral_angle_d	15.8671	572

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 (%)
2-2.07	0.304	140	0.2697	1242	X-RAY DIFFRACTION	98.93
2.07-2.15	0.3589	130	0.2744	1217	X-RAY DIFFRACTION	99.85
2.15-2.25	0.3285	127	0.2574	1238	X-RAY DIFFRACTION	98.48
2.25-2.37	0.3466	148	0.2647	1199	X-RAY DIFFRACTION	98.61
2.37-2.52	0.3016	145	0.2491	1216	X-RAY DIFFRACTION	97.91
2.52-2.71	0.3366	146	0.2515	1217	X-RAY DIFFRACTION	98.63
2.71-2.99	0.3121	155	0.2499	1231	X-RAY DIFFRACTION	98.72
2.99-3.42	0.3056	127	0.2396	1283	X-RAY DIFFRACTION	99.58
3.42-4.31	0.2449	151	0.1732	1281	X-RAY DIFFRACTION	99.58
4.31-40.89	0.2377	137	0.1794	1404	X-RAY DIFFRACTION	99.81

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	4.37950670601	-0.18706980139	-2.43964244119	4.75795845028	3.60270569442	7.91525075053	0.125598362552	0.0948892791449	0.072013321843	-0.438229368161	0.0522821726309	0.209981727669	-1.40670010018	0.68144311914	-0.195825973096	0.565641428849	-0.0495019352703	-0.0802423346167	0.352923392358	-0.0483001612868	0.38532588611	13.3515093507	8.27243830265	9.50602517403
2	3.25276420985	-4.01356951174	-1.57157135183	6.27806783074	0.216737990973	3.17230984109	-0.307636039782	-0.294386408537	0.11461843325	0.288241740756	0.0644031693849	-0.474354238848	-0.0622202132727	1.04340117381	0.0585989067136	0.383630927122	-0.0972766059052	-0.05387971909	0.53048769328	-0.10306546518	0.449343469147	24.8498804791	1.77543009484	9.42703152546
3	2.72921833067	-1.5024500844	-1.56417176879	5.16704463371	2.58048820887	4.39181032292	-0.102683039743	-0.323201538651	0.271073473073	0.368088359747	0.531447943027	-0.79047029434	0.16543602625	0.878665820954	-0.271114515519	0.358772060596	0.0772924623013	-0.097405685821	0.368292828909	0.00277623960893	0.358970336607	19.0862122551	-7.79685997488	10.1310667529
4	2.6093779578	-0.815262448845	-0.791343931338	4.15386897367	1.8079217715	3.78288000709	-0.208309047995	-0.0589894860845	0.0126919522742	0.365829287799	0.0181689048674	0.683064906883	0.25667843407	-0.159027106113	0.228442628752	0.36249079254	-0.0546863900802	0.0298577359839	0.280459394745	0.0131072076444	0.353980363337	-0.366994712599	-1.85873607528	10.8291596969
5	5.01529505015	-2.23158389721	0.281500284867	6.95822752186	1.43089341115	3.02723986739	-0.302135956145	-0.214314951338	-0.333027425375	0.304899359751	0.558392349221	-0.188073081115	0.405732084719	0.575952339734	-0.194560176401	0.465282295233	0.0361847317842	-0.113899765414	0.313062205802	-0.0245949542932	0.330378797679	14.0403752794	-6.82310030182	11.5404012202
6	2.97904299299	-0.7588686091	-0.653294263643	3.47538985822	2.09881702366	3.86374299538	0.033399471119	-0.193849351785	0.00178866275074	0.257504971838	0.132044509556	0.0823321594849	0.173182809033	0.0633328782516	-0.130715204527	0.30380560094	-0.037907731319	-0.02874521645	0.234546846576	0.00694308576856	0.273514318336	5.7390419035	0.111971660378	7.15485971244
7	4.99378499518	0.361235409672	2.26159663104	0.291716166292	0.761275618707	2.24669377126	0.420984592289	-0.429419607808	-0.321103108777	0.574259591291	-0.159642378263	0.224811140273	-0.236748187989	-0.1963371843	-0.127577297958	0.653419334172	-0.0215116374633	0.0513315415805	0.48141407027	0.00807145498875	0.419622350821	-13.5813461973	7.34274639071	5.07613615505
8	9.32553702736	8.18244899696	-4.11211810652	9.71320165505	-6.7269819988	5.60389758889	0.864558530877	0.597077028603	0.988729935186	-0.35054007472	-0.53194774961	0.638054386842	-0.264108478749	-0.0857316990542	-0.366973667359	0.492010791493	0.249665733224	-0.0438894010374	0.647154618161	0.0381221331566	0.452946781942	-21.2899583449	21.3013370333	-8.99732741051
9	9.61754101576	-8.08365859753	-0.815095391634	8.92775087098	1.42796413109	2.92403142574	0.25410495695	0.48382995366	-0.772864729374	-0.19317512566	-0.480033075852	0.953577148142	0.475022721931	-0.514806205124	0.26732264066	0.477930523757	-0.127724536691	-0.0281976592407	0.561214363909	-0.0886869683562	0.447560178666	-21.2686546842	4.35678626585	-2.23080853015

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 100 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 101 through 124 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 125 through 155 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 156 through 179 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 180 through 200 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 201 through 225 )

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