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

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Basic information

Entry
Database: PDB / ID: 6qrd
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-JEH / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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)54,0657
Polymers52,8692
Non-polymers1,1955
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-41 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.532, 76.876, 86.787
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-JEH / 5-azanyl-3-[1-[[4-[(4-propan-2-ylpiperazin-1-yl)methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile


Mass: 453.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31N7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.75→53.51 Å / Num. obs: 51077 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 28.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.014 / Rrim(I) all: 0.042 / Net I/σ(I): 27.2 / Num. measured all: 454004
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.75-1.848.80.37573400.9560.1320.398
5.53-53.517.90.02717810.9990.010.029

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.75→53.51 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.14
RfactorNum. reflection% reflection
Rfree0.2062 2540 4.98 %
Rwork0.1687 --
obs0.1706 51011 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.08 Å2 / Biso mean: 34.6196 Å2 / Biso min: 18.39 Å2
Refinement stepCycle: final / Resolution: 1.75→53.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 83 266 3509
Biso mean--45.11 43.27 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073395
X-RAY DIFFRACTIONf_angle_d1.1094661
X-RAY DIFFRACTIONf_chiral_restr0.041511
X-RAY DIFFRACTIONf_plane_restr0.006590
X-RAY DIFFRACTIONf_dihedral_angle_d16.6271222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7491-1.78280.24221330.190926432776
1.7828-1.81920.20091260.169326742800
1.8192-1.85870.21781290.1726522781
1.8587-1.90190.19631350.164826712806
1.9019-1.94950.20851540.164426382792
1.9495-2.00220.22691330.162426652798
2.0022-2.06110.18841440.17326772821
2.0611-2.12770.20731550.173526602815
2.1277-2.20370.23711400.175426612801
2.2037-2.2920.2041470.171726762823
2.292-2.39630.22811330.171926852818
2.3963-2.52260.2011490.178526772826
2.5226-2.68060.24661260.179927112837
2.6806-2.88760.24481550.186326922847
2.8876-3.17820.23481650.188626782843
3.1782-3.6380.22261340.168827552889
3.638-4.58310.15971370.146727612898
4.5831-53.53660.18551450.163128953040
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)
10.23190.0294-0.07510.1613-0.1450.12390.0324-0.51790.02870.6338-0.18680.0553-0.1797-0.2765-0.00140.3567-0.0006-0.02830.33310.02750.237-32.0592-13.102122.5159
21.1522-0.180.40080.3485-0.45190.72020.105-0.1035-0.09430.21340.105-0.0360.1962-0.185200.2072-0.01270.00970.24410.01650.2579-36.4966-18.678414.1852
31.15910.0230.24670.0392-0.05410.8167-0.022-0.02240.00230.01750.06710.0026-0.0638-0.0383-00.20990.0144-0.0030.2-0.0110.2225-28.1213-10.093211.1629
40.00280.00510.00520.176-0.06010.01240.4745-0.4270.47750.0261-0.36840.07-0.45040.01270.02760.44980.06430.07640.3424-0.08880.3479-14.3863-0.699525.3162
50.12090.0903-0.05470.12510.07560.13370.04390.0246-0.21310.34910.1922-0.27440.05190.1676-0.00020.3250.0423-0.04790.2885-0.03470.30492.3406-4.939241.0477
60.2752-0.12490.18620.133-0.03410.12520.00940.0485-0.0624-0.19270.0632-0.1089-0.16490.1440.00010.2582-0.04410.04740.323-0.05110.24832.6796-2.079324.1992
70.26810.0822-0.08920.2115-0.21360.1971-0.0548-0.2705-0.30620.21750.04190.40990.27-0.32360.00020.348-0.00270.03510.36280.02850.3147-18.6143-22.526534.2693
80.14450.05890.06180.09160.11890.1183-0.1012-0.13280.1677-0.07070.06150.42690.17950.0754-0.00020.30570.0387-0.01050.2597-0.0070.2792-9.5734-5.087442.5228
90.75550.29030.2250.45410.21990.53820.0252-0.0463-0.09490.170.0492-0.11810.12870.0479-0.00010.28630.0464-0.0350.2336-0.00810.2489-7.9867-20.123229.6449
100.007-0.0104-0.03220.11250.09730.0860.00790.1134-0.00910.22230.2213-0.17210.0250.42010.00210.31030.1006-0.06240.2802-0.04320.2878-0.4902-18.466432.9105
110.6305-0.11550.03960.2416-0.31690.3894-0.0294-0.0724-0.05560.05270.0446-0.09690.027-0.0202-0.00010.22020.007-0.00020.2256-0.00570.259-16.3926-19.080817.5136
120.16560.05660.13320.11180.12020.13240.06460.3379-0.3445-0.20760.06880.204-0.1615-0.0640.00240.2899-0.0227-0.02560.3429-0.0680.2887-33.8275-22.2817-6.8318
130.232-0.04450.43070.0479-0.00270.6898-0.04960.5328-0.2489-0.31690.0873-0.2382-0.29020.0045-0.01540.2181-0.03060.05470.5565-0.10130.3487-18.489-19.4269-5.7548
140.08350.0050.0460.0117-0.00380.02420.149-0.36270.28540.0062-0.1912-0.33660.0119-0.401300.28140.01630.05240.3268-0.05580.3918-8.3032-9.47531.818
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 40 )B0 - 40
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 62 )B41 - 62
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 115 )B63 - 115
10X-RAY DIFFRACTION10chain 'B' and (resid 116 through 131 )B116 - 131
11X-RAY DIFFRACTION11chain 'B' and (resid 132 through 183 )B132 - 183
12X-RAY DIFFRACTION12chain 'B' and (resid 184 through 203 )B184 - 203
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 222 )B204 - 222
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 232 )B223 - 232

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