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- PDB-6qo3: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from... -

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Basic information

Entry
Database: PDB / ID: 6qo3
TitleCrystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 2 (5-Amino-3-(2-thienyl) pyrazole)
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
3-thiophen-2-yl-1H-pyrazol-5-amine / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.name

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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)53,2004
Polymers52,8692
Non-polymers3302
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-17 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.304, 79.397, 86.148
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.) Mycobacteroides abscessus (bacteria) / Gene: trmD, MAB_3226c / Production host: Escherichia coli (E. coli)
References: UniProt: B1MDI3, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-J9N / 3-thiophen-2-yl-1H-pyrazol-5-amine / 5-amino-3-(2-thienyl)-pyrazole


Mass: 165.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 48.82 %
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: 1.65→79.4 Å / Num. obs: 62564 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.079 / Net I/σ(I): 14.2 / Num. measured all: 472496 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.737.70.74390220.8090.2840.797100
5.2-79.46.70.05421770.9970.0220.05899.8

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Phasing

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

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Processing

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

6nvr


Resolution: 1.65→56.266 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.83
RfactorNum. reflection% reflection
Rfree0.2072 3248 5.2 %
Rwork0.1745 --
obs0.1762 62491 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.16 Å2 / Biso mean: 31.625 Å2 / Biso min: 12.85 Å2
Refinement stepCycle: final / Resolution: 1.65→56.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 22 314 3599
Biso mean--23.28 43.03 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063384
X-RAY DIFFRACTIONf_angle_d1.0284631
X-RAY DIFFRACTIONf_chiral_restr0.043525
X-RAY DIFFRACTIONf_plane_restr0.006600
X-RAY DIFFRACTIONf_dihedral_angle_d11.9041228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6451-1.66970.35121010.272325922693
1.6697-1.69580.27441590.237725232682
1.6958-1.72360.25341230.228425772700
1.7236-1.75330.23451290.217925332662
1.7533-1.78520.23351240.200925522676
1.7852-1.81950.23871640.186225022666
1.8195-1.85660.21371260.181925782704
1.8566-1.8970.20151380.173725722710
1.897-1.94110.19261600.17425162676
1.9411-1.98970.19751470.166225382685
1.9897-2.04350.19221470.172225652712
2.0435-2.10360.19481590.17425272686
2.1036-2.17150.23441260.172425852711
2.1715-2.24910.22231270.175825762703
2.2491-2.33920.19951390.173425702709
2.3392-2.44570.23291370.172425732710
2.4457-2.57460.18451460.181525832729
2.5746-2.73590.22041270.192525952722
2.7359-2.94710.21551430.19825882731
2.9471-3.24370.20981310.187926112742
3.2437-3.7130.20871600.169326032763
3.713-4.67760.15091680.143526272795
4.6776-56.29910.24681670.165827572924
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)
10.08510.095-0.0080.1169-0.02690.0283-0.07620.6538-0.1114-0.38420.1221-0.08120.1664-0.3181-0.00090.3023-0.02660.01460.3645-0.03130.2896-32.368113.1467-22.8905
21.1101-0.0707-0.00620.3292-0.34330.58230.07660.15230.0459-0.18470.1552-0.1134-0.1604-0.0866-0.00010.22250.0052-0.00290.2464-0.00340.2596-36.204219.3407-14.0566
30.7998-0.2678-0.42060.1522-0.05381.131-0.0781-0.0252-0.0802-0.0870.07320.04290.0306-0.0165-00.2043-0.01380.00710.1934-0.01740.2239-28.99989.8679-10.7567
40.0115-0.0275-0.04940.02350.05550.0907-0.1003-0.2002-0.203-0.10950.0360.07240.09470.1118-00.22470.00810.00410.23050.0110.2234-31.34799.4651-2.6518
50.37270.0927-0.11210.1793-0.17420.1471-0.02110.08110.1024-0.04650.0609-0.0351-0.0947-0.04800.2002-0.01830.0070.2057-0.02460.2135-20.934412.7088-18.4579
60.12430.0809-0.12380.286-0.37350.4949-0.07880.1783-0.2388-0.2232-0.20080.18760.3133-0.113-0.27570.3256-0.0497-0.03810.2686-0.14190.2885-14.19810.628-24.831
70.2567-0.13180.01510.1380.11120.16090.07380.00990.2207-0.33830.0627-0.2484-0.09980.2079-0.00010.3124-0.02190.0350.2580.00130.25012.7794.3187-40.8243
80.28640.0672-0.04360.12310.07620.05790.0046-0.18270.093-0.00040.0666-0.2306-0.05210.12360.00030.22980.0246-0.02040.2762-0.01940.21383.09822.0004-24.1067
90.97380.4001-0.13120.4649-0.06080.67890.00250.201-0.0025-0.0795-0.11950.3854-0.089-0.24270.00010.26520.0294-0.02150.2740.00850.2134-16.534918.2196-35.8228
100.9987-0.3529-0.57630.50050.47850.87290.04460.04030.1306-0.1280.0215-0.0276-0.045-0.0213-00.2394-0.01180.01250.1867-0.00630.2222-8.162719.0697-28.4869
110.02790.05570.00790.06850.02350.0248-0.1336-0.31480.14460.1323-0.0864-0.224-0.29180.1899-0.00030.3570.0078-0.10760.33610.01080.4527-15.362528.4384-10.0442
120.52510.3359-0.28490.7459-0.13210.0367-0.133-0.3640.25370.22840.1563-0.12710.09250.074200.22440.0449-0.04050.3584-0.10970.2521-22.603619.64014.6202
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 115 )A63 - 115
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 131 )A116 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 155 )A132 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 181 )A156 - 181
7X-RAY DIFFRACTION7chain 'A' and (resid 182 through 203 )A182 - 203
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 227 )A204 - 227
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 62 )B0 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 155 )B63 - 155
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 180 )B156 - 180
12X-RAY DIFFRACTION12chain 'B' and (resid 181 through 231 )B181 - 231

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