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

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Basic information

Entry
Database: PDB / ID: 6qqu
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
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(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-JF8 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 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

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)53,3164
Polymers52,8692
Non-polymers4462
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-16 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.410, 78.660, 85.910
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-JF8 / 5-azanyl-3-(1~{H}-indol-6-yl)-1~{H}-pyrazole-4-carbonitrile


Mass: 223.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 48.27 %
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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→58.02 Å / Num. obs: 68474 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.019 / Rrim(I) all: 0.058 / Net I/σ(I): 18.9 / Num. measured all: 605403
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.59-1.639.11.69249860.5710.5891.793100
7.11-58.027.40.0368880.9980.0140.03899.8

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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: 1.59→54.056 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.2
RfactorNum. reflection% reflection
Rfree0.1992 3374 4.93 %
Rwork0.1801 --
obs0.1811 68393 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.46 Å2 / Biso mean: 34.7946 Å2 / Biso min: 18.91 Å2
Refinement stepCycle: final / Resolution: 1.59→54.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 34 249 3461
Biso mean--24.39 44.29 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073329
X-RAY DIFFRACTIONf_angle_d1.074570
X-RAY DIFFRACTIONf_chiral_restr0.043517
X-RAY DIFFRACTIONf_plane_restr0.005592
X-RAY DIFFRACTIONf_dihedral_angle_d11.7361195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.59-1.61270.30381400.275626512791
1.6127-1.63680.27871080.264127072815
1.6368-1.66240.29111320.247626942826
1.6624-1.68960.28511450.252326892834
1.6896-1.71880.27141380.248326832821
1.7188-1.750.26261430.231726892832
1.75-1.78370.24181130.218626692782
1.7837-1.82010.25351110.197427102821
1.8201-1.85970.20741120.197827002812
1.8597-1.90290.20911290.186126922821
1.9029-1.95050.21481530.182926872840
1.9505-2.00330.21751470.174827002847
2.0033-2.06220.2021470.181226582805
2.0622-2.12880.21251310.183427212852
2.1288-2.20490.19661400.179327062846
2.2049-2.29310.2221500.17626662816
2.2931-2.39750.21141580.17927052863
2.3975-2.52390.19581440.184827222866
2.5239-2.6820.24121470.19126972844
2.682-2.88910.23511320.193627352867
2.8891-3.17980.18781430.193127572900
3.1798-3.63990.17141280.180527732901
3.6399-4.58550.17971740.151527502924
4.5855-54.08710.17952090.161328583067
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)
10.217100.02420.1281-0.05010.21260.10140.723-0.176-0.6175-0.35730.05340.0854-0.3617-0.00540.34080.02580.02410.4065-0.01470.2529-32.115913.0997-22.0123
21.2851-0.0466-0.07940.4003-0.35520.70420.0570.11050.006-0.11240.0943-0.0075-0.0703-0.11860.00010.25140.0143-0.01080.29520.00420.2705-36.080118.8159-14.5616
31.3766-0.0123-0.22870.3375-0.01911.1254-0.0416-0.1044-0.0589-0.08820.04310.01320.0608-0.067-0.00010.2328-0.0150.00640.2269-0.00380.2437-29.77289.8208-8.8747
41.0271-0.2842-0.09690.4274-0.48030.4993-0.00260.1942-0.08-0.1435-0.0233-0.01390.0731-0.0819-00.247-0.01920.01680.2524-0.04750.2572-20.69239.1625-20.6208
50.7253-0.2914-0.37230.43330.23170.1613-0.0269-0.07740.1184-0.10010.1237-0.2543-0.07290.3107-00.2857-0.0098-0.00220.2641-0.0150.27812.35153.13-31.1212
60.88860.0624-0.24670.6513-0.48020.51410.27420.39750.2372-0.3578-0.28350.6191-0.2018-0.6305-0.00410.41420.0832-0.03340.35880.01820.3083-17.080720.1592-37.7512
71.0508-0.4671-0.78450.48410.52510.73180.06420.09420.0727-0.2104-0.0198-0.0516-0.1791-0.02100.3001-0.00850.01990.2080.0030.2234-7.571516.6799-31.7202
8-0.02440.0298-0.02490.15620.11940.060.0366-0.11390.0647-0.28680.1029-0.1038-0.19020.3345-0.00010.3038-0.05120.06030.2488-0.0260.2742-0.110317.9124-32.6411
90.6886-0.1129-0.10120.0554-0.25930.6007-0.0217-0.00740.0971-0.0825-0.0044-0.0423-0.0250.0058-00.2194-0.0044-0.00590.2204-0.00620.2605-15.795919.5137-18.5113
100.309-0.2272-0.39860.56340.38260.3274-0.0102-0.37650.15180.17710.0017-0.11420.08090.0092-00.2514-0.0025-0.00590.4479-0.0720.2904-25.881221.52155.9524
110.0576-0.0138-0.01890.01440.0032-0.0050.14610.3692-0.5728-0.13780.1828-0.17340.3788-0.2741-0.00060.2939-0.0542-0.05140.343-0.01210.3826-8.06079.7517-1.6814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 18 )A-1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 62 )A19 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 131 )A63 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 178 )A132 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 227 )A179 - 227
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 48 )B0 - 48
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 115 )B49 - 115
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 131 )B116 - 131
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 182 )B132 - 182
10X-RAY DIFFRACTION10chain 'B' and (resid 183 through 222 )B183 - 222
11X-RAY DIFFRACTION11chain 'B' and (resid 223 through 232 )B223 - 232

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