[English] 日本語
Yorodumi
- PDB-8x6k: The X-ray structure of N-terminal catalytic domain of Thermoplasm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x6k
TitleThe X-ray structure of N-terminal catalytic domain of Thermoplasma acidophilum tRNA methyltransferase Trm56 (Ta0931).
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
tRNA (cytidine(56)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsFukumoto, S. / Hasegawa, T. / Ototake, M. / Moriguchi, S. / Namba, M. / Yamagami, 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
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 2.0Apr 2, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conn
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.pdbx_overall_ESU_R / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Oct 15, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7482
Polymers34,7482
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.074, 110.074, 57.728
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 17373.775 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 36948 / % possible obs: 98.7 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.053 / Net I/σ(I): 30.43
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.38758110.970.4011
1.91-2.040.22455370.9890.2331
2.04-2.210.1351860.9970.1351
2.21-2.420.08847810.9980.0911
2.42-2.70.06443670.9980.0671
2.7-3.120.0538670.9990.0521
3.12-3.810.04232940.9990.0431
3.81-5.380.03926020.9990.0411

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yy8

2yy8


Resolution: 1.802→36.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.92 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1847 5 %RANDOM
Rwork0.1654 35092 --
all0.167 ---
obs-36939 98.701 %-
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: 30.909 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å20.002 Å20 Å2
2--0.005 Å2-0 Å2
3----0.015 Å2
Refinement stepCycle: LAST / Resolution: 1.802→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 8 125 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122508
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162300
X-RAY DIFFRACTIONr_angle_refined_deg1.71.6383394
X-RAY DIFFRACTIONr_angle_other_deg0.6191.5515345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.2191024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02410441
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.74710130
X-RAY DIFFRACTIONr_chiral_restr0.0910.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.2380.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22239
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21271
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2108
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.221
X-RAY DIFFRACTIONr_nbd_other0.160.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.218
X-RAY DIFFRACTIONr_mcbond_it2.9663.0111212
X-RAY DIFFRACTIONr_mcbond_other2.9663.0111212
X-RAY DIFFRACTIONr_mcangle_it3.7764.51515
X-RAY DIFFRACTIONr_mcangle_other3.7774.5041516
X-RAY DIFFRACTIONr_scbond_it4.453.5151296
X-RAY DIFFRACTIONr_scbond_other4.4483.5161297
X-RAY DIFFRACTIONr_scangle_it6.225.0731872
X-RAY DIFFRACTIONr_scangle_other6.2195.0741873
X-RAY DIFFRACTIONr_lrange_it7.53943.0872816
X-RAY DIFFRACTIONr_lrange_other7.54443.0982817
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
1.802-1.8490.2121310.19224890.19327050.9720.97796.85770.159
1.849-1.90.2491320.1825010.18326790.9640.9898.28290.149
1.9-1.9550.2411270.1724180.17425920.9660.98298.18670.142
1.955-2.0150.2191230.1723370.17225120.9730.98297.92990.144
2.015-2.080.211210.16922890.17124540.9720.98398.2070.146
2.08-2.1530.1971150.16822000.1723540.9770.98398.34320.147
2.153-2.2340.1951140.15921580.16123040.9790.98598.61110.141
2.234-2.3250.2021080.16220550.16421900.9720.98498.76710.147
2.325-2.4280.2081060.15820080.1621350.9740.98599.01640.145
2.428-2.5460.201990.16618840.16820010.9770.98499.10050.157
2.546-2.6830.203960.16318330.16519430.9770.98499.27950.156
2.683-2.8450.184920.15717300.15818370.9820.98599.18340.155
2.845-3.040.194850.1716300.17217310.9770.98299.07570.175
3.04-3.2810.203790.16415050.16615900.9750.98499.62260.174
3.281-3.5910.19750.16614180.16714980.980.98599.66620.183
3.591-4.010.179670.16312770.16413490.9810.98599.62940.188
4.01-4.6210.146600.14411390.14412010.9880.98899.83350.178
4.621-5.6370.279520.1729740.17710270.9760.98599.90260.21
5.637-7.8760.259410.2117830.2138250.970.97799.87880.254
7.876-36.030.203240.1544630.1564890.9780.98199.5910.217

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more