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

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Basic information

Entry
Database: PDB / ID: 6qox
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 27 (Methyl 2-(hydroxymethyl)-6H-thieno[2,3-b]pyrrole-5-carboxylate)
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 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
Chem-JA5 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 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 1.0Feb 26, 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)53,0813
Polymers52,8692
Non-polymers2111
Water5,170287
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-16 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.963, 78.460, 88.483
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-JA5 / methyl 2-(hydroxymethyl)-6~{H}-thieno[2,3-b]pyrrole-5-carboxylate


Mass: 211.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
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: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.74→88.48 Å / Num. obs: 54370 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 29.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.017 / Rrim(I) all: 0.047 / Net I/σ(I): 23.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.74-1.8380.79978350.8130.2990.854100
5.5-88.487.30.02419010.9990.0090.02699.8

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Phasing

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

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.15data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→58.705 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2135 2787 5.13 %
Rwork0.1841 --
obs0.1857 54299 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.55 Å2 / Biso mean: 36.9592 Å2 / Biso min: 18.27 Å2
Refinement stepCycle: final / Resolution: 1.74→58.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 14 287 3526
Biso mean--43.99 45.25 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093363
X-RAY DIFFRACTIONf_angle_d1.024611
X-RAY DIFFRACTIONf_chiral_restr0.048523
X-RAY DIFFRACTIONf_plane_restr0.005599
X-RAY DIFFRACTIONf_dihedral_angle_d11.7351225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7389-1.76890.3081140.276925582672
1.7689-1.80110.30421380.255625502688
1.8011-1.83570.29151510.241325312682
1.8357-1.87320.2571350.214825592694
1.8732-1.91390.27691330.205625442677
1.9139-1.95840.23141270.198325342661
1.9584-2.00740.24361360.186225612697
2.0074-2.06170.21931340.192925512685
2.0617-2.12240.20341400.189325662706
2.1224-2.19090.21131500.191225412691
2.1909-2.26920.23011500.183425552705
2.2692-2.360.22131600.182925272687
2.36-2.46740.22711470.187825732720
2.4674-2.59750.22781330.190925612694
2.5975-2.76030.23241290.202825902719
2.7603-2.97340.23111320.206125892721
2.9734-3.27260.21831380.196426102748
3.2726-3.74610.1981420.174126182760
3.7461-4.71930.19331440.148626402784
4.7193-58.73830.18761540.177327542908
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)
12.20190.2983-0.56313.278-0.71642.3897-0.0027-0.26860.02440.32460.09510.0168-0.12320.122-0.11620.20950.00770.00070.2884-0.0270.241335.739693.998214.8897
23.55050.2508-1.96530.02820.05582.1592-0.104-0.0336-0.16010.01460.07290.02880.1375-0.05570.00720.19260.0128-0.01420.18280.02040.204724.331187.461413.2162
31.00870.7503-0.50121.9583-1.25861.3301-0.01820.09550.09050.02540.15340.2419-0.0242-0.4024-0.12690.23420.0225-0.00980.26990.02290.2354-2.687781.881133.0319
43.4461.8661-0.2855.0864-1.64732.23860.0311-0.2760.03460.3587-0.2941-0.6831-0.38880.37120.27330.3361-0.0003-0.01240.3391-0.02330.269716.389296.307937.1069
51.25770.2839-0.71480.9669-0.58262.2497-0.008-0.07260.13530.20630.06590.0557-0.1904-0.0415-0.04360.25550.03930.00280.21150.00670.24219.097798.247227.1266
64.020.9472-1.06190.488-0.30420.2703-0.21250.80270.3317-0.26440.24870.18580.0209-0.1652-0.01160.2802-0.033-0.04180.43780.07450.288323.12797.6486-4.9808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 83 )A0 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 181 )A84 - 181
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 227 )A182 - 227
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 62 )B0 - 62
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 182 )B63 - 182
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 231 )B183 - 231

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