[English] 日本語
Yorodumi
- PDB-6zxy: Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zxy
TitleStructure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransferase enzyme
ComponentstRNA (Guanine(10)-N2)-dimethyltransferase
KeywordsRNA BINDING PROTEIN / tRNA modifications / Epitranscriptomics / Methyltransferase / Heterodimeric enzyme
Function / homology
Function and homology information


tRNA (guanine10-N2)-dimethyltransferase / tRNA (guanine(10)-N2)-dimethyltransferase activity / tRNA (guanine(10)-N2)-methyltransferase activity / tRNA methylation / tRNA binding / RNA binding / cytoplasm
Similarity search - Function
tRNA guanine(10)-N2-dimethyltransferase / Uncharacterized protein family UPF0020 signature. / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / RMKL-like, methyltransferase domain / THUMP domain / THUMP domain / THUMP domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (Guanine(10)-N2)-dimethyltransferase / tRNA (guanine(10)-N2)-dimethyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGraille, M. / Wang, C.
CitationJournal: Nucleic Acids Res.
Title: Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex
Authors: Wang, C. / Tran, N.V. / Jactel, V. / Guerineau, V. / Graille, M.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: tRNA (Guanine(10)-N2)-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9952
Polymers38,9331
Non-polymers621
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint2 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.134, 73.134, 155.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein tRNA (Guanine(10)-N2)-dimethyltransferase


Mass: 38932.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: XD40_1676, XD48_1558
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A117KU88, UniProt: O29011*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Sodium citrate pH 6, 18% PEG 4k, 20% isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 11597 / % possible obs: 99.7 % / Redundancy: 8.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Net I/σ(I): 12.2
Reflection shellResolution: 2.75→2.91 Å / Mean I/σ(I) obs: 1.08 / Num. unique obs: 1808 / CC1/2: 0.462

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZXV
Resolution: 2.75→49.06 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.845 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.076 / SU Rfree Blow DPI: 0.334 / SU Rfree Cruickshank DPI: 0.333
RfactorNum. reflection% reflectionSelection details
Rfree0.255 580 5 %RANDOM
Rwork0.199 ---
obs0.202 11597 99.7 %-
Displacement parametersBiso max: 153.1 Å2 / Biso mean: 80.21 Å2 / Biso min: 45.04 Å2
Baniso -1Baniso -2Baniso -3
1-3.3604 Å20 Å20 Å2
2--3.3604 Å20 Å2
3----6.7209 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.75→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 4 6 2603
Biso mean--114.42 63.19 -
Num. residues----321
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d975SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes451HARMONIC5
X-RAY DIFFRACTIONt_it2667HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion330SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2934SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2667HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3593HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion21.83
LS refinement shellResolution: 2.75→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.253 20 5 %
Rwork0.304 380 -
all0.3015 400 -
obs--94.3 %
Refinement TLS params.Method: refined / Origin x: 18.2776 Å / Origin y: 6.1892 Å / Origin z: 32.0245 Å
111213212223313233
T-0.1692 Å20.035 Å20.0947 Å2--0.1257 Å20.0787 Å2---0.1598 Å2
L3.1334 °2-0.9958 °21.2891 °2-1.5603 °2-0.1202 °2--1.7259 °2
S-0.0848 Å °-0.1774 Å °0.0653 Å °-0.24 Å °0.0665 Å °-0.0778 Å °0.0707 Å °0.1931 Å °0.0184 Å °
Refinement TLS groupSelection details: { B|* }

+
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://pdbjlvh1.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