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

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Basic information

Entry
Database: PDB / ID: 6qrg
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 modification / methylation / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-JET / 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: 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
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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

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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)53,5465
Polymers52,8692
Non-polymers6773
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-26 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.273, 77.867, 86.490
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-JET / [3-(2-methoxy-2-oxidanylidene-ethoxy)phenyl]methyl 1~{H}-pyrazole-4-carboxylate


Mass: 290.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.37 Å3/Da / Density % sol: 48 %
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: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→86.49 Å / Num. obs: 44403 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 37.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Net I/σ(I): 21.1 / Num. measured all: 382304
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.84-1.948.90.79363860.8270.2780.841100
5.81-86.497.90.02915580.9990.0110.03199.8

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.84→38.934 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1962 2205 4.97 %
Rwork0.177 --
obs0.1779 44333 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.02 Å2 / Biso mean: 45.422 Å2 / Biso min: 24.28 Å2
Refinement stepCycle: final / Resolution: 1.84→38.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 47 123 3362
Biso mean--61.76 48.13 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073347
X-RAY DIFFRACTIONf_angle_d1.0174592
X-RAY DIFFRACTIONf_chiral_restr0.043523
X-RAY DIFFRACTIONf_plane_restr0.006597
X-RAY DIFFRACTIONf_dihedral_angle_d13.0141199
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
1.838-1.8780.2841330.258225992732
1.878-1.92170.27491250.231126052730
1.9217-1.96970.23041370.209726032740
1.9697-2.0230.2461640.198825572721
2.023-2.08250.24431340.18425872721
2.0825-2.14970.1911460.1826312777
2.1497-2.22660.20261220.169526142736
2.2266-2.31570.21361510.17925792730
2.3157-2.42110.21081280.184526472775
2.4211-2.54870.23321370.188126092746
2.5487-2.70830.2271470.193626282775
2.7083-2.91740.27651390.203826282767
2.9174-3.21080.21821460.198926392785
3.2108-3.67520.20971320.183426652797
3.6752-4.62910.14341340.143827092843
4.6291-38.94220.15871300.166928282958
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)
11.954-0.36-0.46180.5421-0.52541.27480.0090.23210.025-0.13310.0430.08650.0028-0.2212-00.31120.00510.0060.3630.02810.3263-35.400515.5095-14.8361
21.2397-0.0209-0.5319-0.3602-0.20440.3243-0.06050.0129-0.0429-0.04520.05150.03510.07560.0155-00.3344-0.01610.00140.3159-0.01480.3301-24.0549.0397-13.3669
30.81240.0998-0.09830.66840.47890.4096-0.0124-0.05230.0792-0.12690.1989-0.3373-0.09910.3607-0.00030.341-0.00940.01390.3321-0.01530.28712.66063.4741-32.1609
41.00880.31270.18310.1745-0.07020.5646-0.05160.1503-0.09-0.1413-0.0760.5404-0.0327-0.1399-00.35790.0067-0.01890.34630.01070.3324-15.831317.539-36.6268
51.151-0.2738-0.35370.86950.55470.9608-0.00710.07570.1187-0.24880.02580.01-0.103-0.0214-0.00010.3539-0.03140.00310.2735-0.00060.3073-8.974819.843-26.7118
60.63470.68950.0930.70690.2808-0.3262-0.1242-0.39550.33440.20520.1531-0.06540.08010.0664-00.31180.0318-0.02790.465-0.05010.361-22.488118.744.6836
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 232 )B183 - 232

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