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

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Basic information

Entry
Database: PDB / ID: 6qoc
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 6 (2-(1,3-oxazol-5-yl) aniline)
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE / 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
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
2-(1,3-oxazol-5-yl)aniline / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 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 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 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

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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)53,1904
Polymers52,8692
Non-polymers3202
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-19 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.205, 78.712, 86.601
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 / TRNA (guanine9-N1)-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-J9Q / 2-(1,3-oxazol-5-yl)aniline


Mass: 160.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.84→78.71 Å / Num. obs: 44866 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 35.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Rrim(I) all: 0.056 / Net I/σ(I): 20 / Num. measured all: 339075 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.84-1.947.70.81364250.7770.3120.872100
5.81-78.716.60.03615710.9990.0150.03999.8

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→45.818 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.04
RfactorNum. reflection% reflection
Rfree0.2096 2296 5.12 %
Rwork0.1854 --
obs0.1868 44800 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.89 Å2 / Biso mean: 43.0145 Å2 / Biso min: 23.46 Å2
Refinement stepCycle: final / Resolution: 1.84→45.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 24 185 3412
Biso mean--39.58 48.34 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073336
X-RAY DIFFRACTIONf_angle_d1.0474567
X-RAY DIFFRACTIONf_chiral_restr0.042513
X-RAY DIFFRACTIONf_plane_restr0.006595
X-RAY DIFFRACTIONf_dihedral_angle_d12.6631216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8382-1.87820.35731260.263526152741
1.8782-1.92190.24651480.234326232771
1.9219-1.96990.24991120.202526582770
1.9699-2.02320.23551320.198826072739
2.0232-2.08270.26291270.196826492776
2.0827-2.150.22221390.194726402779
2.15-2.22680.24761360.188626182754
2.2268-2.31590.2191260.196226722798
2.3159-2.42130.23651490.191826182767
2.4213-2.5490.22481560.192726472803
2.549-2.70870.23611390.200526622801
2.7087-2.91780.23471480.209426552803
2.9178-3.21130.2321550.203226472802
3.2113-3.67590.21561340.18827032837
3.6759-4.63050.17391640.152727072871
4.6305-45.83230.18722050.176427832988
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)
10.0716-0.0411-0.2962-0.02450.12110.5810.0778-0.8890.1055-0.10040.01130.0428-0.06120.53630.00270.32040.0253-0.00070.57150.00010.3666106.811692.4532108.5648
21.34270.0948-0.16380.7307-0.1094-0.03510.2947-0.6623-0.1550.7981-0.5052-0.1848-0.80870.7779-0.02320.3834-0.0743-0.00430.4972-0.01610.3471110.816291.278108.4548
30.4620.1544-0.34650.3888-0.32760.510.1453-0.02860.310.25450.11390.3018-0.44990.0331-00.3844-0.04040.05490.3480.01190.4425109.7864106.753492.1331
40.61480.0812-0.21590.35870.07061.01710.0235-0.132-0.26910.0044-0.0105-0.07590.17320.38580.00020.29580.02280.00110.3651-0.00340.3651111.053689.501195.3563
50.81480.06520.04770.16210.24380.4262-0.21740.2669-0.2414-0.17270.0029-0.05560.2666-0.406-0.00540.3126-0.02410.07410.22920.05520.349694.225683.030299.2023
61.41130.4168-1.27460.5169-0.2291.2711-0.11170.0236-0.14970.21270.17930.1150.1098-0.17600.2750.0309-0.00730.2940.00230.3151104.740290.160293.1831
71.26790.2181-0.02830.7930.48020.1967-0.0031-0.27110.0330.0413-0.0259-0.1370.00830.0473-00.29540.03130.00990.30380.05050.262891.933688.3054106.8802
80.54190.06170.03480.1862-0.14460.34070.12270.00150.06190.11480.04940.2143-0.1645-0.285600.40770.06970.080.33040.01840.323271.052283.3254128.3812
90.4372-0.00120.0550.56430.47980.51290.01140.05290.1323-0.0940.11730.5031-0.0319-0.19740.00050.299-0.0265-0.01770.35160.03860.31371.096780.8908110.5544
100.9924-0.66590.02061.3459-0.17081.16740.0639-0.18720.07520.2365-0.1899-0.5021-0.26960.37410.00210.3949-0.02030.01730.39940.00910.315790.630296.7383122.6735
111.32840.3615-0.68780.6923-1.06481.46970.0697-0.07860.18420.21710.11040.1319-0.084-0.0152-0.00010.38420.02410.06090.2839-0.0030.311379.99398.5343117.1888
120.4869-0.56750.0640.86260.8991.06330.0192-0.01570.10310.1967-0.02790.07580.02290.08930.00020.2855-0.0040.01110.26510.02410.30290.151398.0441104.6898
130.6375-0.5578-0.40680.5996-0.04340.3861-0.00950.41780.2417-0.16460.08080.06940.0238-0.0588-00.2786-0.0115-0.02280.41390.07680.302197.10197.672781.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )A0 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 40 )A18 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 62 )A41 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 83 )A63 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 100 )A84 - 100
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 131 )A101 - 131
7X-RAY DIFFRACTION7chain 'A' and (resid 132 through 183 )A132 - 183
8X-RAY DIFFRACTION8chain 'A' and (resid 184 through 203 )A184 - 203
9X-RAY DIFFRACTION9chain 'A' and (resid 204 through 228 )A204 - 228
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 62 )B0 - 62
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 131 )B63 - 131
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 182 )B132 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 231 )B183 - 231

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