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

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Basic information

Entry
Database: PDB / ID: 6qrf
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 modification / methylation / cytoplasm
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
(phenylmethyl) 1~{H}-pyrazole-4-carboxylate / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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: J.Med.Chem. / Year: 2019
Title: Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Authors: Whitehouse, A.J. / Thomas, S.E. / Brown, K.P. / Fanourakis, A. / Chan, D.S. / Libardo, M.D.J. / Mendes, V. / Boshoff, H.I.M. / Floto, R.A. / Abell, C. / Blundell, T.L. / Coyne, A.G.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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)53,7747
Polymers52,8692
Non-polymers9055
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-25 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.820, 78.610, 84.830
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-JF5 / (phenylmethyl) 1~{H}-pyrazole-4-carboxylate


Mass: 202.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H10N2O2
#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.: 177 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
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: 1.86→57.66 Å / Num. obs: 42198 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.022 / Rrim(I) all: 0.065 / Net I/σ(I): 18 / Num. measured all: 367671
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.86-1.918.41.56130750.6450.571.664100
8.32-57.667.40.0255540.9990.010.02799.6

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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: 1.86→45.441 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.59
RfactorNum. reflection% reflection
Rfree0.2171 2096 4.98 %
Rwork0.186 --
obs0.1876 42125 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.48 Å2 / Biso mean: 46.7285 Å2 / Biso min: 24 Å2
Refinement stepCycle: final / Resolution: 1.86→45.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 65 177 3397
Biso mean--58.94 49.4 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073334
X-RAY DIFFRACTIONf_angle_d0.9944566
X-RAY DIFFRACTIONf_chiral_restr0.04515
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d14.2431201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.86-1.90330.42251510.332825992750
1.9033-1.95090.29061560.282626222778
1.9509-2.00370.30461520.245226132765
2.0037-2.06260.27411440.220326312775
2.0626-2.12920.28291360.207426452781
2.1292-2.20530.24441260.194626492775
2.2053-2.29360.25291160.196626742790
2.2936-2.3980.23011120.189326802792
2.398-2.52440.22121300.189226412771
2.5244-2.68250.20671370.192426752812
2.6825-2.88960.26611270.208826722799
2.8896-3.18030.2551330.211126932826
3.1803-3.64040.21421150.188627172832
3.6404-4.58580.16511410.150227432884
4.5858-45.45420.19522200.166527752995
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)
11.63930.2965-0.83625.7761-0.21982.1361-0.0021.03250.0714-0.96360.22220.1690.0683-0.5466-0.00490.4466-0.0062-0.00420.65280.03770.4099-32.319313.9422-21.8253
22.1847-0.119-0.57422.67591.11413.23510.12830.4060.0451-0.53070.1175-0.0032-0.3539-0.1888-0.050.36580.02080.02010.46250.07530.4437-35.709319.0244-14.6845
32.4791-0.1823-1.24170.83840.20372.0106-0.04210.0429-0.1189-0.13780.0657-0.04330.1412-0.11010.06150.2942-0.0233-0.00560.3189-0.00650.3288-29.58449.4216-9.084
42.9223-0.1666-0.7051.69340.10971.8349-0.05140.26560.0967-0.2398-0.01550.19340.0737-0.23860.01530.3311-0.02110.00920.328-0.03240.2995-19.479.5376-20.4127
51.3191-0.0619-0.65751.55470.69980.9042-0.0237-0.05010.1252-0.12340.2613-0.4068-0.11890.3834-0.00550.3349-0.01550.02610.336-0.02580.33562.72253.3834-31.4804
62.63270.5517-0.36092.96020.39642.2569-0.04490.11370.3381-0.04280.03070.8615-0.4692-0.4481-0.08290.48950.0984-0.0050.45090.0450.429-18.004323.7814-34.0779
74.9326-2.0402-1.51748.89540.50040.4965-0.1777-0.011-0.1654-0.29180.14860.6817-0.01490.0778-0.11280.3532-0.05610.00530.3211-0.01620.3098-8.81043.8922-40.6671
81.1871-0.3458-0.89680.86060.62282.06450.03830.08110.2615-0.29560.0501-0.1174-0.30480.0284-0.15940.3912-0.02760.01790.27110.0090.354-5.630120.124-30.1666
91.3870.0942-0.95610.9133-0.57621.6526-0.0450.0190.2602-0.1271-0.0262-0.0084-0.1565-0.1192-0.09180.30910.0124-0.02890.2948-0.020.3613-15.406719.6857-18.489
103.0331-0.1942-0.76950.52050.1390.6107-0.1464-0.43940.21690.19790.1478-0.05430.04280.0989-0.06150.3196-0.0119-0.00850.4257-0.06230.4029-22.1319.18024.545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )A0 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 62 )A18 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 131 )A63 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 180 )A132 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 227 )A181 - 227
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 40 )B0 - 40
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 62 )B41 - 62
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 131 )B63 - 131
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 181 )B132 - 181
10X-RAY DIFFRACTION10chain 'B' and (resid 182 through 232 )B182 - 232

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