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- PDB-6qr9: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from... -

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Basic information

Entry
Database: PDB / ID: 6qr9
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
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(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-JEE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 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)53,6944
Polymers52,8692
Non-polymers8252
Water1,13563
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-18 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.679, 77.179, 87.556
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-JEE / 5-azanyl-3-[1-[[4-(morpholin-4-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile


Mass: 412.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
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: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.42→77.18 Å / Num. obs: 20277 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 37.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.083 / Rrim(I) all: 0.245 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.42-2.558.51.37328930.6760.4971.462100
7.64-77.187.20.0787240.9960.0290.08499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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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: 2.42→54.036 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2461 963 4.76 %
Rwork0.1818 --
obs0.1849 20225 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.63 Å2 / Biso mean: 42.1764 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 2.42→54.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 62 63 3296
Biso mean--41.65 43.48 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083321
X-RAY DIFFRACTIONf_angle_d1.1484546
X-RAY DIFFRACTIONf_chiral_restr0.042506
X-RAY DIFFRACTIONf_plane_restr0.005584
X-RAY DIFFRACTIONf_dihedral_angle_d16.41189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4169-2.54430.32331180.227327102828
2.5443-2.70370.28891250.230927202845
2.7037-2.91250.27831590.207827102869
2.9125-3.20550.23521290.191727112840
3.2055-3.66930.2631480.17527402888
3.6693-4.62250.22011330.153527782911
4.6225-54.04910.22491510.176128933044
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)
11.0780.50670.9132.20541.07162.19510.053-0.45240.15740.31160.0613-0.08930.0028-0.3069-0.15590.33030.07560.04010.62330.00380.3566-32.9116-10.09425.2968
21.48020.1110.53951.07190.6292.4150.0627-0.2988-0.1790.21120.240.04410.383-0.0005-0.23880.2474-0.0236-0.010.34860.06990.3328-37.3619-23.2999.8956
31.79970.28610.71050.8522-0.07871.8985-0.0043-0.08310.09310.10330.0264-0.0451-0.1604-0.036-0.03850.23420.0204-0.00260.2257-0.01250.2319-28.3238-10.165811.206
43.16-1.63620.68570.9906-0.47050.23340.1299-0.51350.73330.713-0.11440.0157-0.3559-0.1758-0.08050.50230.00170.18770.4441-0.14470.3334-18.0757-0.311626.1377
51.45070.3602-0.49391.54070.07881.24190.0192-0.0158-0.29490.3550.1485-0.2688-0.2060.1807-0.13750.31370.0242-0.03280.326-0.03350.30181.9595-4.781440.2537
61.54460.56190.0133.70892.55463.09690.05580.0941-0.173-0.5142-0.03130.0132-0.29060.05-0.23610.2444-0.02770.00140.3326-0.03710.24522.5347-1.919324.3291
72.2125-2.0062-0.6834.93481.53862.1751-0.2079-0.0755-0.42760.08030.1980.67380.5658-0.22830.1410.4032-0.0073-0.00860.27740.0260.3893-19.6276-22.956432.339
83.26672.122.70947.32673.9964.1354-0.1551-0.5338-0.08890.5014-0.01040.4583-0.13770.0007-0.04740.39590.00910.03090.43640.10690.2068-15.7228-18.416643.0332
90.20510.48320.28731.21330.96621.3109-0.0014-0.0565-0.15310.37350.0293-0.0720.40550.1492-0.02010.29280.0419-0.04630.2199-0.00430.2809-7.8137-16.811731.9722
100.46990.75340.08281.29470.49531.1340.0517-0.0391-0.09330.17890.0401-0.04920.26960.0596-0.01510.3160.04660.00080.276-0.02930.2818-9.4999-17.939326.674
111.40840.55110.62291.0235-0.83281.73-0.51240.0141-0.0545-0.12830.07010.05320.68110.3722-0.07880.4050.08460.08550.2504-0.00650.3225-20.0217-23.2093.3163
121.90380.3267-0.07730.8792-0.28450.2488-0.08010.3733-0.2207-0.30640.12-0.0971-0.00260.0305-0.02740.3092-0.0210.0210.4037-0.04660.2451-23.1738-19.0382-5.1003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 29 )A-1 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 62 )A30 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 155 )A63 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 179 )A156 - 179
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 203 )A180 - 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 48 )B30 - 48
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 116 )B49 - 116
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 155 )B117 - 155
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 184 )B156 - 184
12X-RAY DIFFRACTION12chain 'B' and (resid 185 through 231 )B185 - 231

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