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- PDB-6qo4: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from... -

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Basic information

Entry
Database: PDB / ID: 6qo4
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 3 (2-(5-Isoxazolyl) phenol)
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 (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
2-(1,2-oxazol-5-yl)phenol / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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 1.3Jan 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)53,1924
Polymers52,8692
Non-polymers3222
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-18 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.487, 78.902, 86.272
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-97T / 2-(1,2-oxazol-5-yl)phenol


Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
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: 1.78→78.9 Å / Num. obs: 49667 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.78-1.877.70.88171770.7760.3340.944
5.62-78.96.60.04317410.9980.0170.047

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Phasing

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

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.15data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.78→58.224 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.77
RfactorNum. reflection% reflection
Rfree0.2134 2382 4.8 %
Rwork0.18 --
obs0.1816 49599 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.95 Å2 / Biso mean: 39.7469 Å2 / Biso min: 20.93 Å2
Refinement stepCycle: final / Resolution: 1.78→58.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 24 226 3483
Biso mean--31.74 45.44 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073358
X-RAY DIFFRACTIONf_angle_d1.0724596
X-RAY DIFFRACTIONf_chiral_restr0.043515
X-RAY DIFFRACTIONf_plane_restr0.006599
X-RAY DIFFRACTIONf_dihedral_angle_d11.7241215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7775-1.81380.3071510.289126942845
1.8138-1.85320.28331410.244727562897
1.8532-1.89630.27891250.216327612886
1.8963-1.94380.27671220.202627342856
1.9438-1.99630.21641090.187727752884
1.9963-2.05510.25241630.195427432906
2.0551-2.12140.21631380.187227552893
2.1214-2.19720.22631390.18727472886
2.1972-2.28520.19651320.182327462878
2.2852-2.38920.22941570.178427782935
2.3892-2.51520.2031530.183127222875
2.5152-2.67280.25331400.188927852925
2.6728-2.87910.251300.204627902920
2.8791-3.16880.25121500.202227952945
3.1688-3.62730.22511470.184428002947
3.6273-4.56980.17771440.145728462990
4.5698-58.25490.17271410.167129903131
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)
10.1487-0.14560.9002-0.0236-0.17860.87690.1296-0.69080.00850.1313-0.0647-0.3406-0.0501-0.6328-0.00130.3525-0.0007-0.02850.5748-0.00580.3024-32.3004-14.153622.7027
20.25920.06480.30840.10920.00310.5825-0.46050.8639-0.0950.3221-0.66990.55270.3882-0.7898-0.01470.98950.24610.25630.7911-0.00420.9103-33.8911-0.544930.5984
31.93260.07860.31251.0976-0.98541.12090.145-0.5132-0.31260.17250.09420.20610.4033-0.3304-0.00010.3309-0.08670.0180.42260.0680.3027-40.0663-21.739513.7978
41.44770.76421.82941.09270.56862.06360.0625-0.1116-0.0850.03210.0952-0.02160.047-0.18430.00010.2271-0.00590.01680.28330.01680.2867-34.5417-16.69576.361
51.89190.22570.73110.1226-0.34221.5344-0.26170.10460.4164-0.1434-0.03980.079-0.31970.252-0.00020.2827-0.0116-0.05030.2159-0.03840.3278-20.0171-4.359912.6483
62.48840.78831.52310.6697-0.08221.70030.0062-0.1253-0.04840.33030.07990.01750.1577-0.05140.00040.25720.040.00530.2808-0.0210.264-29.5397-13.982410.9792
70.0552-0.02230.3758-0.23830.00210.5185-0.09280.28640.34630.0866-0.0218-0.0545-0.14390.1108-0.00040.24220.01270.01480.2450.02010.2848-31.4646-9.13192.6456
82.14971.19380.49130.6668-0.63050.13920.054-0.25720.05080.1460.01440.0618-0.0246-0.074900.28940.01590.00730.2839-0.05740.2515-18.43-9.63120.0423
90.72750.5934-0.49680.4592-0.14850.790.1239-0.096-0.09460.3049-0.0054-0.20110.13590.2287-0.00010.37390.053-0.07980.2941-0.02670.30222.7866-4.640641.3158
101.25480.29770.25970.0743-0.20230.65060.00660.1931-0.1456-0.10350.0825-0.35740.07160.163400.2782-0.0270.03010.3103-0.0370.29473.1364-2.30124.1639
110.7196-0.4559-0.29050.15450.09980.43370.05440.1407-0.24270.1637-0.09770.4950.4579-0.4276-0.00020.4012-0.0335-0.03790.37570.01960.3569-19.0323-22.070832.3248
121.0552-0.9665-0.37180.52140.08620.92820.1738-0.2757-0.26980.6815-0.72680.96980.9481-0.8658-0.02290.4125-0.1222-0.02040.3375-0.00890.436-20.0765-26.516332.7359
130.6450.4133-0.0570.77470.09630.23140.0131-0.19730.21490.16520.0390.32170.0846-0.1001-0.00110.35650.0108-0.04560.3619-0.01250.3213-10.3404-5.617643.3435
141.1126-0.2327-0.14911.44681.57750.6020.07170.0083-0.20180.1890.0673-0.17060.17770.1468-0.00020.3288-0.001-0.06490.2282-0.01760.2863-6.6066-21.533828.6946
151.44560.60571.30780.23450.87562.0201-0.1718-0.1406-0.1527-0.17730.14130.1843-0.1351-0.0756-0.00110.3777-0.0096-0.04790.30470.0240.2641-9.6936-17.028531.5945
160.08890.47590.19210.60730.14240.08510.0814-0.0801-0.00610.34620.0954-0.03590.06630.08370.00010.34610.0485-0.0620.2767-0.04420.2943-0.1618-18.573333.0136
170.8133-0.60970.09221.2552-1.81731.11430.07660.0846-0.1630.22240.0555-0.06770.0421-0.0818-0.00010.2163-0.00960.00190.2389-0.02750.2721-16.2323-19.200117.2464
181.698-0.61850.00571.2305-0.1936-0.49940.07820.3274-0.2794-0.13150.0007-0.1082-0.00530.0264-00.2527-0.00840.02250.3952-0.06530.2439-22.7561-19.0799-5.1478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )A1 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 30 )A20 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 50 )A31 - 50
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 83 )A51 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 100 )A84 - 100
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 115 )A101 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 131 )A116 - 131
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 182 )A132 - 182
9X-RAY DIFFRACTION9chain 'A' and (resid 183 through 203 )A183 - 203
10X-RAY DIFFRACTION10chain 'A' and (resid 204 through 227 )A204 - 227
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 16 )B0 - 16
12X-RAY DIFFRACTION12chain 'B' and (resid 17 through 40 )B17 - 40
13X-RAY DIFFRACTION13chain 'B' and (resid 41 through 62 )B41 - 62
14X-RAY DIFFRACTION14chain 'B' and (resid 63 through 100 )B63 - 100
15X-RAY DIFFRACTION15chain 'B' and (resid 101 through 115 )B101 - 115
16X-RAY DIFFRACTION16chain 'B' and (resid 116 through 131 )B116 - 131
17X-RAY DIFFRACTION17chain 'B' and (resid 132 through 183 )B132 - 183
18X-RAY DIFFRACTION18chain 'B' and (resid 184 through 231 )B184 - 231

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