6ZXW | pdb_00006zxw

Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex bound to sinefungin

PDB DOI: https://doi.org/10.2210/pdb6ZXW/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: 2.19 Å
R-Value Free:
0.217 (Depositor), 0.230 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

(2020) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 45.76 kDa
Atom Count: 3,187
Modeled Residue Count: 378
Deposited Residue Count: 386
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (Guanine(10)-N2)-dimethyltransferase	A [auth G]	326	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: XD40_1676, XD48_1558 EC: 2.1.1.213
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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	B [auth H]	60	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: XD40_0284, XD48_0149
UniProt
Find proteins for A0A117KMN5 (Archaeoglobus fulgidus) Explore A0A117KMN5 Go to UniProtKB: A0A117KMN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A117KMN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG Query on SFG Download Ideal Coordinates CCD File SDF format, chain C [auth G] MOL2 format, chain C [auth G] mmCIF format, chain C [auth G]	C [auth G]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain C [auth G] Interactions & Density Focus chain C [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth G] SDF format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth G]	P [auth G], Q [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth G] Focus chain Q [auth G] Interactions & Density Focus chain P [auth G] Focus chain Q [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain R [auth H] MOL2 format, chain R [auth H] mmCIF format, chain R [auth H]	R [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth H] Interactions & Density Focus chain R [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain H [auth G] SDF format, chain L [auth G] SDF format, chain O [auth G] SDF format, chain N [auth G] SDF format, chain M [auth G] SDF format, chain I [auth G] SDF format, chain G SDF format, chain D [auth G] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain H [auth G] MOL2 format, chain L [auth G] MOL2 format, chain O [auth G] MOL2 format, chain N [auth G] MOL2 format, chain M [auth G] MOL2 format, chain I [auth G] MOL2 format, chain G MOL2 format, chain D [auth G] mmCIF format, chain E [auth G] mmCIF format, chain F [auth G] mmCIF format, chain H [auth G] mmCIF format, chain L [auth G] mmCIF format, chain O [auth G] mmCIF format, chain N [auth G] mmCIF format, chain M [auth G] mmCIF format, chain I [auth G] mmCIF format, chain G mmCIF format, chain D [auth G]	D [auth G] E [auth G] F [auth G] G H [auth G] D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], L [auth G], M [auth G], N [auth G], O [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Interactions & Density Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G]	J [auth G], K [auth G]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain J [auth G] Focus chain K [auth G]