9U0O | pdb_00009u0o

Priestia megaterium isoleucyl-tRNA synthetase 2 in complex with Escherichia coli tRNA-Ile-GAU and ATP

PDB DOI: https://doi.org/10.2210/pdb9U0O/pdb

Classification: TRANSLATION
Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581, Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-01-28 Released: 2026-09-16
Deposition Author(s): Modrusan, P., Brkic, A., Lecona Butelli, A., Leibundgut, M., Zivkovic, I., Ban, N., Longo, L.M., Gruic-Sovulj, I.
Funding Organization(s): Swiss National Science Foundation, Croatian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 5.30 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

C-terminal evolutionary remodelling of isoleucyl-tRNA synthetases is a prokaryote-specific strategy for tuning aminoacylation rate

Modrusan, P., Brkic, A., Lecona Butelli, A., Leibundgut, M., Zivkovic, I., Ban, N., Longo, L.M., Gruic-Sovulj, I.

To be published.

Macromolecule Content

Total Structure Weight: 571.81 kDa
Atom Count: 39,884
Modeled Residue Count: 4,436
Deposited Residue Count: 4,436
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoleucine--tRNA ligase	A, B, C, D	1,032	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 0 Gene Names: ileS, BG04_5198 EC: 6.1.1.5
UniProt
Find proteins for A0A0B6AVD3 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore A0A0B6AVD3 Go to UniProtKB: A0A0B6AVD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0B6AVD3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
tRNA-Ile-GAU (77-MER)	E [auth a], F [auth b], G [auth c], H [auth d]	77	Escherichia coli K-12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth d] MOL2 format, chain R [auth d] mmCIF format, chain R [auth d]	R [auth d]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth d] Interactions & Density Focus chain R [auth d]