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

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Basic information

Entry
Database: PDB / ID: 6qqy
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 / 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
Chem-JD2 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 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)53,4984
Polymers52,8692
Non-polymers6292
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-14 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.510, 78.450, 86.040
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-JD2 / 5-azanyl-3-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile


Mass: 314.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 48.28 %
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: 1.49→57.97 Å / Num. obs: 82944 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 24.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.016 / Rrim(I) all: 0.047 / Net I/σ(I): 21.9 / Num. measured all: 728911
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.49-1.538.71.62260280.5140.5711.723100
6.66-57.977.60.0310490.9990.0120.03299.5

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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: 1.49→54.026 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.1904 4117 4.97 %
Rwork0.1752 --
obs0.176 82867 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.62 Å2 / Biso mean: 32.5105 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: final / Resolution: 1.49→54.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 48 326 3577
Biso mean--23.85 43.55 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063399
X-RAY DIFFRACTIONf_angle_d1.0454669
X-RAY DIFFRACTIONf_chiral_restr0.041523
X-RAY DIFFRACTIONf_plane_restr0.006605
X-RAY DIFFRACTIONf_dihedral_angle_d13.7581236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.49-1.50750.35341250.294326682793
1.5075-1.52590.26841430.269927002843
1.5259-1.54520.27351650.256726442809
1.5452-1.56560.25491420.241526972839
1.5656-1.5870.25151360.226226852821
1.587-1.60970.22751230.219226792802
1.6097-1.63370.25661250.207626952820
1.6337-1.65930.23271330.213827242857
1.6593-1.68650.19731360.207927172853
1.6865-1.71550.23841460.194426472793
1.7155-1.74670.21721220.188127202842
1.7467-1.78030.1921400.180626842824
1.7803-1.81670.2021290.1727242853
1.8167-1.85620.19341380.173526892827
1.8562-1.89940.18721430.172627002843
1.8994-1.94690.20261390.174926922831
1.9469-1.99950.20771570.169427052862
1.9995-2.05830.18051380.175527122850
2.0583-2.12480.18191510.171327132864
2.1248-2.20070.18181290.169327262855
2.2007-2.28880.19691360.168927012837
2.2888-2.3930.19421310.171827492880
2.393-2.51920.22491350.180927482883
2.5192-2.6770.19671550.182526972852
2.677-2.88370.19241420.188227522894
2.8837-3.17390.21681600.184727432903
3.1739-3.6330.18071680.172827482916
3.633-4.57690.15981590.14627912950
4.5769-54.06120.1741710.169429003071
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)
10.2244-0.0091-0.01260.0463-0.04480.16670.11280.5363-0.2062-0.3952-0.30740.06740.207-0.179-0.00020.31960.00910.00230.3546-0.01460.2488-32.206912.9895-22.1215
21.1070.00290.01140.2959-0.22030.5980.04330.1476-0.0172-0.13770.09850.0234-0.0948-0.0849-00.2371-0.003-0.0140.27310.00410.2614-35.96618.5976-14.6768
31.4737-0.1884-0.65730.1578-0.13350.8126-0.0514-0.0025-0.0638-0.02380.03110.01370.0632-0.0538-0.00010.2017-0.0175-0.0040.1938-0.01270.2072-27.839410.3732-11.1308
40.04640.00030.01050.1361-0.12110.0814-0.04320.4837-0.3474-0.189-0.24460.11860.19790.0832-0.01730.5160.0172-0.11030.3747-0.11920.3839-19.7932-0.6295-26.6753
50.4603-0.20580.23640.42530.16040.28510.0535-0.03230.0724-0.20260.0971-0.1632-0.05890.16050.00040.3211-0.03460.03920.2458-0.01430.23881.64174.2848-39.283
60.47030.2029-0.22220.14950.10220.1527-0.0859-0.1370.17460.00220.1662-0.2010.00690.33920.00020.27050.04-0.02810.3055-0.03560.2692.85572.0916-23.9047
71.36080.2682-0.61310.4809-0.18220.57380.01740.339-0.0339-0.236-0.07480.3392-0.0957-0.2254-0.00030.290.0253-0.03640.28560.00170.2105-14.757615.5168-38.0321
80.688-0.3274-0.58640.36170.56290.7460.07360.0510.1131-0.18580.0428-0.099-0.18780.00430.00010.2894-0.0160.02260.20860.00060.2429-7.66920.1959-29.7583
90.0275-0.03650.01030.14280.0270.04560.0836-0.02170.0693-0.23190.1321-0.089-0.10720.18310.00020.293-0.05250.05690.2386-0.0290.2649-0.328418.0229-32.6691
100.25330.0906-0.18830.1011-0.16240.2360.05530.06660.0868-0.0391-0.08930.09390.034-0.0685-00.2255-0.0006-0.00010.222-0.01370.2448-15.698217.1601-22.0539
110.09660.0767-0.0240.1050.07850.1147-0.077-0.34920.16650.0123-0.126-0.3386-0.30590.2326-0.00510.2775-0.0039-0.05360.26590.02070.4371-16.48325.2995-7.2061
120.1001-0.0546-0.11270.08370.13060.2190.031-0.30520.24720.1278-0.02760.10890.1375-0.08930.00010.23970.01250.00250.3094-0.05820.2387-33.219422.72366.4139
130.23370.0521-0.39280.0144-0.07350.4917-0.1317-0.41810.31710.51010.2127-0.49770.30630.0495-0.0270.22950.0362-0.07060.4789-0.08910.3355-18.165120.11235.9216
140.0837-0.0152-0.02020.00050.00230.00310.0760.221-0.312-0.11210.1069-0.15040.2428-0.4343-0.00090.2642-0.042-0.03850.3078-0.02170.345-7.97899.7601-1.7096
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 155 )A63 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 178 )A156 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 203 )A179 - 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 115 )B63 - 115
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 131 )B116 - 131
10X-RAY DIFFRACTION10chain 'B' and (resid 132 through 155 )B132 - 155
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 182 )B156 - 182
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 203 )B183 - 203
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 222 )B204 - 222
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 232 )B223 - 232

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