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

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Basic information

Entry
Database: PDB / ID: 6nvr
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in Apo form
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / TrmD / tRNA methyltransferase / SPOUT methyltransferase
Function / homology
Function and homology information


tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol
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
: / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.562 Å
AuthorsThomas, S.E. / Whitehouse, A.J. / Coyne, A.G. / Abell, C. / Mendes, V.M. / 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 5, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 19, 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


Theoretical massNumber of molelcules
Total (without water)52,8692
Polymers52,8692
Non-polymers00
Water6,287349
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-17 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.724, 79.128, 86.235
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.) Mycobacteroides abscessus (bacteria) / Gene: trmD, DDJ36_03475 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2T7GQ66, UniProt: B1MDI3*PLUS, tRNA (guanine37-N1)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 48.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.08 mM 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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.56→86.23 Å / Num. obs: 72241 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 27.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.019 / Rrim(I) all: 0.053 / Net I/σ(I): 20.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.56-1.657.40.729104560.8350.2850.784100
4.94-86.237.10.04524930.9980.0180.04899.9

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QUV

3quv


Resolution: 1.562→58.303 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.1943 3548 4.92 %
Rwork0.1806 --
obs0.1813 72159 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.99 Å2 / Biso mean: 35.4464 Å2 / Biso min: 19.32 Å2
Refinement stepCycle: final / Resolution: 1.562→58.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 0 349 3663
Biso mean---44.06 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063443
X-RAY DIFFRACTIONf_angle_d1.0274721
X-RAY DIFFRACTIONf_chiral_restr0.042536
X-RAY DIFFRACTIONf_plane_restr0.006614
X-RAY DIFFRACTIONf_dihedral_angle_d11.6851270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5619-1.58330.28511210.246627642885
1.5833-1.60590.26051440.23726832827
1.6059-1.62990.25441240.217627202844
1.6299-1.65540.21011330.208727152848
1.6554-1.68250.22781270.198527352862
1.6825-1.71150.21041210.200627462867
1.7115-1.74260.23721450.201826982843
1.7426-1.77620.25111460.197327162862
1.7762-1.81240.20381270.193926962823
1.8124-1.85180.21131400.194527212861
1.8518-1.89490.23471590.182127542913
1.8949-1.94230.23091380.182327082846
1.9423-1.99480.1951430.179227202863
1.9948-2.05350.21931690.183627072876
2.0535-2.11980.19821390.186127272866
2.1198-2.19560.22131330.181727382871
2.1956-2.28350.19321400.187227402880
2.2835-2.38740.20211370.183627592896
2.3874-2.51330.20751100.189527702880
2.5133-2.67070.23161480.191827492897
2.6707-2.8770.21791720.200227432915
2.877-3.16650.21981450.19927862931
3.1665-3.62460.19471590.180727672926
3.6246-4.56630.1451770.149427862963
4.5663-58.34350.17251510.16829633114
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)
10.0883-0.0659-0.00420.0679-0.10940.2369-0.0446-0.65770.12430.2601-0.0252-0.1362-0.1064-0.3757-0.00050.32130.0034-0.02050.4458-0.03580.3069-32.2082-13.261722.7664
21.71710.00910.13860.6072-0.57161.09440.0726-0.239-0.04110.22540.12560.0120.2066-0.0610.00010.2474-0.0222-0.00090.31350.01720.2697-35.9338-18.850914.3374
31.90510.22810.75430.1157-0.07341.4568-0.0252-0.01620.12990.05620.02950.0027-0.0638-0.02200.22030.008600.2057-0.0150.2446-27.319-10.423611.0677
40.13680.0131-0.0170.0977-0.12050.1615-0.1058-0.56170.10150.4095-0.31370.4105-0.33-0.0534-0.02980.52960.01390.12020.5109-0.17660.5281-19.21990.825526.5516
50.0171-0.034-0.03660.09950.09270.055-0.1568-0.0917-0.00350.1841-0.1031-0.1027-0.1944-0.15420.00030.34080.0177-0.01670.2667-0.02360.2272-1.7245-4.36436.1894
60.699-0.0464-0.07930.42740.11380.0373-0.01010.0895-0.09940.05840.1312-0.30610.08560.22940.00010.27390.0003-0.0090.2761-0.01330.26263.7745-2.759830.306
71.2109-0.8411-0.02050.887-0.04720.87560.0188-0.1594-0.11930.1915-0.14740.40340.149-0.2766-0.00010.3228-0.03620.0090.30.02350.2452-16.6002-17.997436.0323
80.85430.33060.39080.74520.42750.73070.0775-0.0335-0.16990.14020.0525-0.09360.08210.0315-0.00010.29350.0187-0.02790.2139-0.00930.2361-5.7237-19.545330.5343
90.9337-0.35740.11780.89-0.13550.40930.00830.1037-0.11480.07730.0416-0.0470.05220.07170.00010.1937-0.01120.02070.2014-0.02420.2289-20.867-20.474912.6292
100.37190.15880.32380.7417-0.44940.3503-0.09420.3687-0.3612-0.37450.2232-0.3118-0.09810.2266-0.00060.2569-0.01510.05920.4979-0.14980.3491-22.143-21.7868-7.2732
110.06660.00990.04260.0156-0.01080.0140.1899-0.2080.835-0.01880.0169-0.3141-0.3068-0.4858-0.00050.26360.0270.04830.3271-0.05790.3988-8.0929-9.9221.4777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )A0 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 62 )A20 - 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 188 )A179 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 227 )A189 - 227
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 62 )B0 - 62
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 131 )B63 - 131
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 191 )B132 - 191
10X-RAY DIFFRACTION10chain 'B' and (resid 192 through 222 )B192 - 222
11X-RAY DIFFRACTION11chain 'B' and (resid 223 through 232 )B223 - 232

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