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

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Basic information

Entry
Database: PDB / ID: 6qqt
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 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
Chem-JCH / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.673 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)53,6986
Polymers52,8692
Non-polymers8294
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-33 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.591, 77.862, 86.636
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-JCH / 3-[1-[(4-methoxyphenyl)methyl]indol-6-yl]-1~{H}-pyrazol-5-amine


Mass: 318.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18N4O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 48.3 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.67→86.64 Å / Num. obs: 58996 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 30.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Rrim(I) all: 0.054 / Net I/σ(I): 20.7 / Num. measured all: 519445 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.67-1.768.80.91285210.7860.3260.97100
5.29-86.647.80.04420560.9980.0170.04799.9

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.673→45.743 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.43
RfactorNum. reflection% reflection
Rfree0.2052 2867 4.87 %
Rwork0.1712 --
obs0.1729 58921 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.47 Å2 / Biso mean: 38.7664 Å2 / Biso min: 18.97 Å2
Refinement stepCycle: final / Resolution: 1.673→45.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 58 231 3454
Biso mean--42.19 46.98 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063349
X-RAY DIFFRACTIONf_angle_d0.9754599
X-RAY DIFFRACTIONf_chiral_restr0.042518
X-RAY DIFFRACTIONf_plane_restr0.006591
X-RAY DIFFRACTIONf_dihedral_angle_d12.531204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6728-1.70170.27361500.250527762926
1.7017-1.73260.26131380.234927772915
1.7326-1.76590.2171470.208427492896
1.7659-1.8020.22291400.203827682908
1.802-1.84120.23721400.194927722912
1.8412-1.8840.22761290.192927652894
1.884-1.93110.22571480.176227782926
1.9311-1.98330.18781440.165727752919
1.9833-2.04170.21281480.17127732921
2.0417-2.10760.19851540.164527632917
2.1076-2.18290.19241300.171627952925
2.1829-2.27030.191250.169728172942
2.2703-2.37360.21871450.171527902935
2.3736-2.49880.20131320.174628062938
2.4988-2.65530.21711460.183128122958
2.6553-2.86030.19631410.19328222963
2.8603-3.14810.21651510.192428072958
3.1481-3.60340.21731650.173628232988
3.6034-4.53930.191420.142528863028
4.5393-45.76020.19361520.162930003152
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)
11.40310.0165-0.75462.71050.11051.97530.08650.7234-0.1522-0.6501-0.2691-0.13970.3853-0.36120.01740.34850.01110.00370.4460.02450.2665-32.116213.0225-22.3404
22.21540.0274-0.61961.74250.60782.51560.05850.29860.048-0.2520.09250.0547-0.1541-0.2309-0.02460.27530.0007-0.02520.32570.03560.3156-36.236718.8024-14.2449
32.1483-0.0612-0.65160.57560.19711.5921-0.06930.0509-0.087-0.03240.06650.03380.1157-0.05460.04120.229-0.0212-0.00550.2212-0.00850.2299-27.768510.1106-11.3473
44.51811.525-0.20171.001-0.43760.368-0.10290.2722-0.5547-0.4625-0.30680.01920.4906-0.1545-0.2630.4936-0.1311-0.09860.396-0.22620.3438-14.27620.6532-25.2112
51.3158-0.4964-0.39831.7953-0.33631.33710.0556-0.00490.1569-0.59220.1595-0.5519-0.08760.2602-0.02830.3937-0.07120.07450.3133-0.02610.28932.35194.7863-41.0487
61.4103-0.9624-1.43533.04232.71293.5315-0.0634-0.16520.06110.28030.2153-0.20120.25280.3326-0.06040.2970.0296-0.05010.3683-0.02210.2752.77612.0399-24.2203
72.36110.2505-0.64621.80050.5861.95120.14910.01110.24840.3742-0.03550.7108-0.104-0.7986-0.07040.44840.0218-0.00630.46490.04290.3981-19.707323.7196-31.3361
82.5847-0.5039-1.31390.12630.05324.60380.0830.72960.5056-0.74320.17070.301-0.1792-0.1922-0.2230.42090.0184-0.06270.49910.05560.3468-16.732722.4631-38.8789
94.5631-0.7969-1.29794.21861.19790.962-0.13940.4941-0.3114-0.2519-0.00250.7611-0.1808-0.2131-0.07550.3591-0.0424-0.01350.3499-0.02520.2864-9.51114.6521-42.1762
101.3972-0.3207-0.70921.1230.68262.21970.01490.13230.158-0.31010.0383-0.0793-0.2421-0.0328-0.15390.2966-0.0440.00940.2428-0.00230.2544-7.825520.2025-29.6198
111.4108-0.3072-1.02971.15941.2832.0095-0.0134-0.04170.0141-0.44920.2675-0.2147-0.13410.3374-0.19480.3416-0.09520.03890.2892-0.01420.3053-0.331418.7527-33.1868
121.5078-0.3224-0.99090.5603-0.63762.02910.03220.03780.2399-0.0336-0.0112-0.0322-0.1816-0.1347-0.09950.2427-0.0064-0.0230.2694-0.01950.3131-16.010419.376-18.2038
132.3754-0.125-0.61611.0650.0031.60780.0813-0.59610.62610.4186-0.00670.25460.13070.1118-0.05540.30890.03630.00770.3901-0.07990.3451-33.548722.46326.4016
142.4245-1.3584-1.75153.86913.324.0923-0.2428-0.77170.44440.71980.3597-0.27780.24250.1919-0.14550.29210.0249-0.06780.5512-0.08730.3639-18.640519.5036.2275
155.0679-2.80270.63693.2536-1.32925.1240.18080.1936-0.6976-0.0977-0.0231-0.33590.6329-0.2041-0.04040.3339-0.0385-0.03330.3564-0.05480.4726-8.25089.7159-1.6476
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 181 )A156 - 181
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 203 )A182 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 227 )A204 - 227
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 29 )B0 - 29
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 40 )B30 - 40
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 62 )B41 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 115 )B63 - 115
11X-RAY DIFFRACTION11chain 'B' and (resid 116 through 131 )B116 - 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 222 )B204 - 222
15X-RAY DIFFRACTION15chain 'B' and (resid 223 through 232 )B223 - 232

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