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

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Basic information

Entry
Database: PDB / ID: 6qoo
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 18 (Isoxazole-5-carbothioamide)
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 TrmD / 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
1,2-oxazole-5-carbothioamide / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 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)53,2225
Polymers52,8692
Non-polymers3523
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-29 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.574, 80.037, 84.737
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-JAB / 1,2-oxazole-5-carbothioamide


Mass: 128.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2OS
#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.: 133 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.94→80.04 Å / Num. obs: 37822 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 37.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Rrim(I) all: 0.078 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.94-2.047.80.79154420.8460.30.847100
6.13-80.046.40.04513310.9980.0180.04999.9

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→58.185 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.68
RfactorNum. reflection% reflection
Rfree0.2289 2017 5.34 %
Rwork0.1784 --
obs0.181 37754 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.08 Å2 / Biso mean: 46.2637 Å2 / Biso min: 24.19 Å2
Refinement stepCycle: final / Resolution: 1.94→58.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 21 133 3378
Biso mean--68.29 49.34 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073349
X-RAY DIFFRACTIONf_angle_d1.0464590
X-RAY DIFFRACTIONf_chiral_restr0.042522
X-RAY DIFFRACTIONf_plane_restr0.005597
X-RAY DIFFRACTIONf_dihedral_angle_d12.6951211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.939-1.98750.31381430.258824982641
1.9875-2.04120.2961340.229125482682
2.0412-2.10130.28521620.22124862648
2.1013-2.16910.26971610.213424932654
2.1691-2.24670.24271280.198425342662
2.2467-2.33660.27951300.188325372667
2.3366-2.4430.23181320.191425432675
2.443-2.57180.24411570.18825382695
2.5718-2.73290.25181540.200125222676
2.7329-2.94390.25341360.201925692705
2.9439-3.24010.2371450.193525542699
3.2401-3.70890.23141290.175325862715
3.7089-4.67260.1731360.14426232759
4.6726-58.21150.22261700.163827062876
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)
12.6762-1.25423.45950.9277-1.62444.88460.29531.0414-0.0545-0.3886-0.1150.09130.1580.6629-0.12660.37330.05340.08540.7046-0.010.356233.3687-13.6209-22.1919
22.5813-0.57852.13740.7334-0.33392.3369-0.02090.0920.0034-0.1460.0722-0.0734-0.02840.1531-0.07370.2623-0.0270.04550.2771-0.00350.272724.8063-12.4361-13.7979
32.146-0.3585-0.52282.6413-0.64710.8793-0.0599-0.191-0.1035-0.09360.22390.38170.133-0.1506-0.1520.29920.0066-0.04020.34490.0120.3104-4.1012-1.6087-28.1707
41.5617-2.07791.43982.8478-2.04961.76760.08760.2287-0.4835-0.0709-0.1028-0.60210.37880.61940.04760.47280.0762-0.02970.452-0.05960.465220.3459-26.3596-29.7089
52.5315-0.10270.50443.5463-2.05893.97370.01150.4601-0.018-0.98310.1107-0.12590.31840.20020.04560.68730.03810.04490.5299-0.08190.324915.277-17.0798-43.9348
61.4771-0.63881.00881.5886-1.26771.56520.03940.0967-0.1383-0.32230.01890.10260.1104-0.0159-0.04260.34-0.0069-0.04880.2178-0.02030.27548.1395-17.695-28.0817
73.18620.8379-0.33670.78110.06991.17560.1639-0.9006-0.76860.29780.1106-0.04340.0230.1313-0.00990.2661-0.0004-0.04070.53470.10830.382731.9094-23.07586.0223
82.1372-1.41420.34151.2912-0.18230.19690.0543-0.7684-0.51110.32380.00270.468-0.13520.31630.11680.2655-0.02620.0450.50760.10650.409214.6612-17.50843.8719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 40 )A0 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 191 )A41 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 227 )A192 - 227
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 30 )B0 - 30
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 48 )B31 - 48
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 180 )B49 - 180
7X-RAY DIFFRACTION7chain 'B' and (resid 181 through 203 )B181 - 203
8X-RAY DIFFRACTION8chain 'B' and (resid 204 through 231 )B204 - 231

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