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

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Basic information

Entry
Database: PDB / ID: 6qqs
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / 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
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(1~{H}-indol-6-yl)-1~{H}-pyrazol-5-amine / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsThomas, S.E. / Whitehouse, A.J. / Coyne, A.G. / Abell, C. / Mendes, V. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateCystic Fibrosis Trust Registered Charity No. (England and Wales) 1079049, Registered Charity No. (Scotland) SC040196 United Kingdom
CitationJournal: 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, ...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, C. / Coyne, A.G. / Blundell, T.L. / Floto, R.A. / Mendes, V.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: 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 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2664
Polymers52,8692
Non-polymers3962
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-15 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.357, 79.028, 85.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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-JCZ / 3-(1~{H}-indol-6-yl)-1~{H}-pyrazol-5-amine


Mass: 198.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.76→74.36 Å / Num. obs: 50911 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 30.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.857.60.90473540.750.3490.97100
5.56-74.366.60.04817790.9980.020.05299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.76→54.154 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.12
RfactorNum. reflection% reflection
Rfree0.2119 2372 4.67 %
Rwork0.1775 --
obs0.1791 50842 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.05 Å2 / Biso mean: 38.8348 Å2 / Biso min: 20.28 Å2
Refinement stepCycle: final / Resolution: 1.76→54.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 30 186 3348
Biso mean--27.37 46.37 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073273
X-RAY DIFFRACTIONf_angle_d0.9844492
X-RAY DIFFRACTIONf_chiral_restr0.042510
X-RAY DIFFRACTIONf_plane_restr0.005580
X-RAY DIFFRACTIONf_dihedral_angle_d11.6211173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7578-1.79370.28241290.2728542983
1.7937-1.83270.26151300.248227952925
1.8327-1.87530.27051270.220528222949
1.8753-1.92220.22541190.195328492968
1.9222-1.97420.19721270.185828342961
1.9742-2.03230.22721120.191128372949
2.0323-2.09790.25951610.188827922953
2.0979-2.17290.21971400.178528132953
2.1729-2.25990.22131560.170628342990
2.2599-2.36270.18051550.169728072962
2.3627-2.48730.19641500.171228242974
2.4873-2.64320.23951440.187928542998
2.6432-2.84720.24181520.200128432995
2.8472-3.13370.24421350.198328663001
3.1337-3.58710.21611190.178629083027
3.5871-4.5190.18631770.15128843061
4.519-54.18010.19151390.166530543193
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.9266-0.3174-0.99753.1230.71562.7240.09890.8412-0.147-0.8545-0.3095-0.3830.0999-0.49360.02650.3367-0.00920.02860.46820.01680.2868-32.242613.7853-22.0704
23.03950.002-0.99231.5160.06492.0526-0.00990.373-0.0159-0.27170.07840.1829-0.0993-0.30920.0330.2426-0.0047-0.0210.3280.04280.2637-36.182416.5896-12.6427
32.75780.3043-0.45932.32241.47353.4491-0.11170.0304-0.440.1785-0.0508-0.02920.44050.07660.04840.3011-0.00390.04090.281-0.02090.315-19.8174.627-12.6489
42.6014-0.539-1.53370.11920.09391.1675-0.05870.1213-0.0928-0.07430.0460.01830.0671-0.06020.04470.2367-0.0375-0.0210.2531-0.03120.2265-24.652410.829-13.6469
51.6277-0.8542-0.22042.3692-0.9351.80740.09030.27280.0035-0.82860.1367-0.4019-0.05970.40520.00030.3789-0.06340.06910.3185-0.03480.28533.14964.2014-41.3408
62.1368-0.8497-1.28963.53192.2452.95640.0662-0.19380.14720.08860.0955-0.39770.04560.1985-0.00630.25220.0127-0.05360.3162-0.01150.28532.71831.9889-23.9127
72.6044-1.3668-0.57552.94110.58931.7603-0.080.2983-0.0037-0.3746-0.01660.4894-0.2907-0.2393-0.06640.33470.0123-0.05350.31070.01230.2592-14.624716.3102-37.4874
81.3354-0.3542-0.86821.24790.95762.01720.03570.0480.2349-0.34210.0365-0.0676-0.27180.0144-0.15340.266-0.0237-0.00630.2169-0.00470.2394-8.675719.5396-26.7951
93.2821-0.2073-0.88390.86440.05690.1222-0.1526-0.5630.19180.24890.1805-0.14390.04580.1082-0.05390.28240.0249-0.02390.4319-0.05680.2882-22.59419.15594.5874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 83 )A19 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 100 )A84 - 100
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 183 )A101 - 183
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 203 )A184 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 227 )A204 - 227
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 62 )B0 - 62
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 182 )B63 - 182
9X-RAY DIFFRACTION9chain 'B' and (resid 183 through 232 )B183 - 232

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