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- PDB-9sdw: tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 9sdw
TitletRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus in complex with SAM-competitive compound
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / TrmD / Inhibitor / m7G / S. aureus
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / cytosol
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 TrmD / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
: / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWeldert, A.C. / Hof, F. / Huebner, A.F. / Wolf, E. / Barthels, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Nanoscale Direct-to-Biology Optimization and Structural Insights into Selective S. aureus TrmD Inhibitors.
Authors: Hubner, A.F. / Weldert, A.C. / Marciniak, T. / Hof, F. / Beck, V.S. / Carien, S. / Mulartschyk, S.N. / Wolf, E. / Ziebuhr, W. / Barthels, F.
History
DepositionAug 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3462
Polymers30,0591
Non-polymers2871
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14390 Å2
Unit cell
Length a, b, c (Å)126.875, 126.875, 126.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 30059.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: trmD, SAS1174 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6G9X3, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-A1JNG / 1-[2-[4-(4-oxidanylidene-3,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)-1,2,3-triazol-1-yl]ethyl]guanidine


Mass: 287.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N9O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.83 Å3/Da / Density % sol: 56.55 % / Description: Cubic crystal grew within 2 weeks
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 8mg/mL protein in 1.4M Na Malonate pH 7.4, 0.1M Bis-Tris Propane

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Nov 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→56.74 Å / Num. obs: 11305 / % possible obs: 100 % / Redundancy: 79.6 % / Biso Wilson estimate: 59.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.099 / Net I/σ(I): 44.7
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.973 / Num. unique obs: 1340 / CC1/2: 0.971 / Rpim(I) all: 0.106 / Rrim(I) all: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.86 Å / SU ML: 0.3669 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2913 566 5.02 %
Rwork0.2275 10700 -
obs0.2303 11266 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 21 30 1883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661894
X-RAY DIFFRACTIONf_angle_d1.00012567
X-RAY DIFFRACTIONf_chiral_restr0.0528279
X-RAY DIFFRACTIONf_plane_restr0.0086337
X-RAY DIFFRACTIONf_dihedral_angle_d5.7624255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.860.33441400.25342594X-RAY DIFFRACTION99.93
2.86-3.270.30821440.28432609X-RAY DIFFRACTION99.96
3.28-4.130.30331440.2312654X-RAY DIFFRACTION100
4.13-44.860.27021380.20492843X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.949349855142 Å / Origin y: 19.660555416664 Å / Origin z: 39.38795149972 Å
111213212223313233
T0.3699900568782 Å2-0.17149326882142 Å2-0.06674335739177 Å2-0.69315326972489 Å2-0.041916831799186 Å2--0.21106687590737 Å2
L0.45184480208499 °20.14924025940717 °21.130201345727 °2-0.21752664765721 °20.081414922068166 °2--0.94607737232952 °2
S-0.50520017985833 Å °0.60898579522856 Å °-0.076673548251811 Å °-0.17961565667388 Å °0.3311889348569 Å °-0.014354758862767 Å °-0.39012318656868 Å °0.67304885244057 Å °-0.20510049078987 Å °
Refinement TLS groupSelection details: all

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