6ZXY

Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransferase enzyme

PDB DOI: https://doi.org/10.2210/pdb6ZXY/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-07-30 Released: 2020-09-23
Deposition Author(s): Graille, M., Wang, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.255
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex

Wang, C., Tran, N.V., Jactel, V., Guerineau, V., Graille, M.

(null) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 38.99 kDa
Atom Count: 2,625
Modelled Residue Count: 321
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (Guanine(10)-N2)-dimethyltransferase	A [auth B]	340	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: XD40_1676, XD48_1558
UniProt
Find proteins for O29011 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29011 Go to UniProtKB: O29011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O29011
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B	B	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.255
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.134	α = 90
b = 73.134	β = 90
c = 155.09	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.