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

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Basic information

Entry
Database: PDB / ID: 6qod
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 7 (2-Amino-6-fluorobenzothiazole)
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 (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
6-fluoro-1,3-benzothiazol-2-amine / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.852 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 1.0Mar 4, 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)53,2064
Polymers52,8692
Non-polymers3362
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-15 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.143, 78.379, 86.540
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-FBB / 6-fluoro-1,3-benzothiazol-2-amine


Mass: 168.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5FN2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 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: 1.85→86.54 Å / Num. obs: 43636 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.031 / Rrim(I) all: 0.086 / Net I/σ(I): 15.8 / Num. measured all: 329136 / Scaling rejects: 210
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.957.60.97462760.7020.3781.04699.9
5.86-86.546.50.04315370.9980.0180.04699.8

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.852→56.305 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2116 2243 5.15 %
Rwork0.1843 --
obs0.1858 43566 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 37.7858 Å2 / Biso min: 17.9 Å2
Refinement stepCycle: final / Resolution: 1.852→56.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 22 185 3392
Biso mean--51.92 42.38 -
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073320
X-RAY DIFFRACTIONf_angle_d1.0144551
X-RAY DIFFRACTIONf_chiral_restr0.042514
X-RAY DIFFRACTIONf_plane_restr0.006591
X-RAY DIFFRACTIONf_dihedral_angle_d11.3221196
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
1.8518-1.89210.36051370.307325252662
1.8921-1.93610.32431220.274625552677
1.9361-1.98450.28941170.235625662683
1.9845-2.03820.24991290.211125852714
2.0382-2.09810.25941300.200725422672
2.0981-2.16590.24551400.205925682708
2.1659-2.24330.22641280.179625692697
2.2433-2.33310.22531220.182925682690
2.3331-2.43930.22761410.18325582699
2.4393-2.56790.19811650.18525552720
2.5679-2.72880.2271190.199826022721
2.7288-2.93940.26961520.203725822734
2.9394-3.23520.22731520.197625902742
3.2352-3.70330.19571340.175426222756
3.7033-4.66540.17541600.144626192779
4.6654-56.33060.18061950.17427172912
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)
10.6064-0.6589-1.03771.16632.14074.17380.08370.6019-0.1976-0.2864-0.05920.09920.1619-0.46340.01250.2927-0.0248-0.01750.4767-0.05460.285-32.390311.0885-24.1916
23.1103-1.7949-1.65395.78892.14313.069-0.02420.29630.0927-0.17180.00640.3153-0.2765-0.2930.02920.27090.0351-0.01630.32570.05150.2369-40.354620.1997-15.0448
32.0652-0.13210.10642.78421.61124.28120.0420.03310.4608-0.19620.0087-0.0679-0.3879-0.0016-0.07130.19580.03750.03420.25570.02220.2971-34.997622.1874-4.9083
43.2472-0.3063-0.79190.28530.64772.9437-0.12010.0704-0.2657-0.12350.11140.01890.12490.05540.01220.2187-0.01530.01260.1714-0.00430.2385-26.368.3698-11.6399
52.3102-0.0809-0.94820.26740.11382.0156-0.0666-0.0021-0.0731-0.06810.061-0.05980.04590.0886-0.01520.1963-0.0006-0.00550.1761-0.01410.2082-25.388911.23-11.6077
63.74490.8508-0.37570.8035-0.88651.09670.01780.0819-0.495-0.2621-0.35540.1159-0.01570.0851-0.4420.38490.0283-0.07770.2292-0.14730.3247-10.87860.7821-25.0115
71.4871-0.47330.29823.1573-0.0551.38570.14560.13580.2238-0.66320.0458-0.5316-0.22670.2885-0.05590.3511-0.04810.08250.2705-0.02930.25112.69294.4742-41.2446
81.3888-0.9034-1.12613.49452.75612.3138-0.0846-0.25910.15770.27470.2082-0.3260.07240.3061-0.14780.29270.0488-0.04880.3293-0.0240.2472.88362.2581-23.7875
93.2050.8185-0.28893.58251.24093.2390.1844-0.01650.22980.1244-0.35080.6952-0.3701-0.59990.14950.31810.05810.00180.3162-0.03110.3039-19.133622.0208-32.5542
102.6405-0.8651-1.04490.96830.58662.38990.03810.19880.064-0.4484-0.04040.37-0.3097-0.4426-0.04260.32450.0274-0.03160.3292-0.01020.2617-14.401315.6175-38.7119
111.3413-0.3451-0.66091.17931.1332.64650.10070.12240.1821-0.30850.037-0.1085-0.20990.0503-0.07780.2397-0.01870.03440.1637-0.00350.1902-5.767119.8612-30.7649
121.4281-0.4578-0.91170.9753-0.6613.16120.0056-0.06170.1203-0.1109-0.0938-0.0187-0.0873-0.20130.15850.1813-0.0054-0.01260.2332-0.02460.2538-15.837619.3591-18.49
132.51820.1284-0.04651.7043-0.00651.38040.0685-0.54880.44710.2494-0.05970.04140.1096-0.1021-0.06930.25770.01060.02620.3521-0.08810.2966-33.112222.63336.4495
142.2065-0.6598-0.81861.4340.12410.8037-0.1295-0.51770.4540.21980.1867-0.31850.1207-0.1482-0.05560.22780.0222-0.06170.4441-0.11010.3419-15.138916.88413.5756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 29 )A0 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 48 )A30 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 73 )A49 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 115 )A74 - 115
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 155 )A116 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 182 )A156 - 182
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 203 )A183 - 203
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 228 )A204 - 228
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 16 )B0 - 16
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 62 )B17 - 62
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 131 )B63 - 131
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 182 )B132 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 203 )B183 - 203
14X-RAY DIFFRACTION14chain 'B' and (resid 204 through 231 )B204 - 231

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