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- PDB-9u46: The X-ray structure of N-terminal catalytic domain of Thermoplasm... -

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Basic information

Entry
Database: PDB / ID: 9u46
TitleThe X-ray structure of N-terminal catalytic domain of Thermoplasma acidophilum tRNA methyltransferase Trm56 (Ta0931) in complex with 5'-Methylthioadenosine
ComponentstRNA (cytidine(56)-2'-O)-methyltransferase
KeywordsTRANSFERASE / 2'-O methylation / SPOUT superfamily / Archaea
Function / homology
Function and homology information


tRNA (cytidine56-2'-O)-methyltransferase / tRNA (cytidine(56)-2'-O)-methyltransferase activity / tRNA nucleoside ribose methylation / cytoplasm
Similarity search - Function
tRNA ribose 2'-O-methyltransferase, aTrm56 / tRNA ribose 2'-O-methyltransferase, aTrm56 / HDIG domain / HD domain profile. / HD domain / HD domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / tRNA (cytidine(56)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 Å
AuthorsFukumoto, S. / Hasegawa, T. / Ototake, M. / Moriguchi, S. / Namba, M. / Yamagamai, R. / Kawamura, T. / Hirata, A. / Hori, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Transfer RNA Recognition Mechanism of Thermoplasma acidophilum Trm56, a SPOUT tRNA Methyltransferase that Possesses an Unusually Long C-terminal Region.
Authors: Hidetaka, S. / Fukumoto, S. / Hasegawa, T. / Kawamura, T. / Ototake, M. / Moriguchi, S. / Namba, M. / Tomikawa, C. / Yamagami, R. / Hirata, A. / Hori, H.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 2, 2025ID: 8X6J
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (cytidine(56)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6712
Polymers17,3741
Non-polymers2971
Water95553
1
A: tRNA (cytidine(56)-2'-O)-methyltransferase
hetero molecules

A: tRNA (cytidine(56)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3424
Polymers34,7482
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4100 Å2
ΔGint-15 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 71.400, 86.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein tRNA (cytidine(56)-2'-O)-methyltransferase / tRNA ribose 2'-O-methyltransferase aTrm56


Mass: 17373.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: DSM 1728 / Gene: Ta0931 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2
References: UniProt: Q9HJN6, tRNA (cytidine56-2'-O)-methyltransferase
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 10241 / % possible obs: 99.4 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.19
Reflection shellResolution: 1.99→2.11 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 8.57 / Num. unique obs: 1613 / CC1/2: 0.97 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YY8

2yy8


Resolution: 1.992→39.083 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.388 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2243 512 5 %
Rwork0.1709 9729 -
all0.173 --
obs-10241 99.485 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.892 Å2
Baniso -1Baniso -2Baniso -3
1--1.054 Å2-0 Å2-0 Å2
2--2.16 Å20 Å2
3----1.106 Å2
Refinement stepCycle: LAST / Resolution: 1.992→39.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 20 53 1295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121266
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161152
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6391709
X-RAY DIFFRACTIONr_angle_other_deg0.561.5522671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.0121012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40210217
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.491064
X-RAY DIFFRACTIONr_chiral_restr0.0750.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_nbd_refined0.2360.2252
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21119
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2642
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.217
X-RAY DIFFRACTIONr_nbd_other0.1860.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.213
X-RAY DIFFRACTIONr_mcbond_it2.3472.365603
X-RAY DIFFRACTIONr_mcbond_other2.3382.365603
X-RAY DIFFRACTIONr_mcangle_it3.3193.537752
X-RAY DIFFRACTIONr_mcangle_other3.3173.54753
X-RAY DIFFRACTIONr_scbond_it3.7612.886663
X-RAY DIFFRACTIONr_scbond_other3.7582.889664
X-RAY DIFFRACTIONr_scangle_it5.3254.137957
X-RAY DIFFRACTIONr_scangle_other5.3224.14958
X-RAY DIFFRACTIONr_lrange_it7.14535.4911440
X-RAY DIFFRACTIONr_lrange_other7.14235.481440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.992-2.0430.237360.1656900.1697500.9690.98296.80.142
2.043-2.0990.16360.1696860.1687230.9790.98199.86170.15
2.099-2.160.257350.1696750.1747100.9570.9811000.148
2.16-2.2260.294350.1726570.1786920.9530.9811000.153
2.226-2.2990.197340.1596360.1616710.9750.98499.8510.14
2.299-2.3790.222320.156130.1546460.9650.98599.84520.135
2.379-2.4680.294310.1595870.1656180.9490.9841000.143
2.468-2.5690.239300.1795710.1826010.9560.981000.168
2.569-2.6830.212290.1825510.1845800.9690.9791000.167
2.683-2.8130.253280.1675340.1715630.9620.98399.82240.157
2.813-2.9640.193260.1754910.1765170.9720.9811000.169
2.964-3.1430.334250.184850.1855100.9420.9811000.177
3.143-3.3580.295240.1994510.2044760.9550.97599.78990.202
3.358-3.6250.228220.184200.1834450.9660.98199.32580.189
3.625-3.9680.177210.1633930.1644150.9840.98599.7590.176
3.968-4.430.169180.153460.1513670.9820.98799.18260.169
4.43-5.1050.186170.1613260.1623450.9810.98899.42030.184
5.105-6.2250.202140.212680.212850.9890.97998.94740.234
6.225-8.6950.216120.1722170.1742340.9810.98397.86320.187
8.695-39.0830.23970.151320.1541450.9810.96995.86210.203

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