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

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Basic information

Entry
Database: PDB / ID: 9sdv
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
Chem-21X / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)30,4353
Polymers30,0591
Non-polymers3762
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint2 kcal/mol
Surface area13960 Å2
Unit cell
Length a, b, c (Å)126.695, 126.695, 126.695
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-21X / N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide


Mass: 314.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.82 Å3/Da / Density % sol: 56.37 % / 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: 2.5→56.66 Å / Num. obs: 12606 / % possible obs: 100 % / Redundancy: 78.9 % / Biso Wilson estimate: 51.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.063 / Net I/σ(I): 66.6
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.466 / Num. unique obs: 1378 / CC1/2: 0.993 / Rpim(I) all: 0.054 / Rrim(I) all: 0.469 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.23 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2804 608 4.84 %
Rwork0.2224 11956 -
obs0.2252 12564 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.54 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 26 58 1903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961893
X-RAY DIFFRACTIONf_angle_d1.19012568
X-RAY DIFFRACTIONf_chiral_restr0.0639279
X-RAY DIFFRACTIONf_plane_restr0.0148338
X-RAY DIFFRACTIONf_dihedral_angle_d6.0045261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.33971450.25842917X-RAY DIFFRACTION99.93
2.75-3.150.35971420.29072921X-RAY DIFFRACTION99.97
3.15-3.970.2981500.22352970X-RAY DIFFRACTION100
3.97-42.230.24081710.19573148X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.095146786939 Å / Origin y: 19.603205790184 Å / Origin z: 39.437246385652 Å
111213212223313233
T0.48718447688936 Å2-0.18374533734373 Å2-0.036588049853816 Å2-0.73275852907428 Å2-0.0049844798294536 Å2--0.34507598925533 Å2
L1.9682640901189 °20.84556372031583 °21.9890626307596 °2-0.67235016455041 °20.73789998965906 °2--2.0062791195836 °2
S-0.51563216033669 Å °0.75827564041541 Å °0.10661206401995 Å °-0.31505283567234 Å °0.4161999217115 Å °-0.081390325368389 Å °-0.50136796398331 Å °0.89475680908958 Å °0.051891971390936 Å °
Refinement TLS groupSelection details: all

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