8AFJ

tRNA modifying enzyme MiaE soaked in Na-dithionite in a glovebox and flash-cooled using a miniature-airlock

PDB DOI: https://doi.org/10.2210/pdb8AFJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-18 Released: 2023-03-29
Deposition Author(s): van der Linden, P., Engilberge, S., Atta, M., Carpentier, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.228
R-Value Work: 0.200
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

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

Literature

tRNA modifying enzyme MiaE soaked in Na-dithionite in a glovebox and flash-cooled using a miniature-airlock

van der Linden, P., Engilberge, S., Atta, M., Carpentier, P.

To be published.

Macromolecule Content

Total Structure Weight: 46.5 kDa
Atom Count: 3,443
Modelled Residue Count: 394
Deposited Residue Count: 400
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 hydroxylase	A [auth B], B [auth A]	200	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: AYO08_21560, CBL13_00280, CBP06_18695
UniProt
Find proteins for A0A179QS89 (Pseudomonas putida) Explore A0A179QS89 Go to UniProtKB: A0A179QS89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A179QS89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain M [auth A] MOL2 format, chain E [auth B] MOL2 format, chain M [auth A]	E [auth B], M [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth B] Focus chain M [auth A] Interactions & Density Focus chain E [auth B] Focus chain M [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain F [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	F [auth B], N [auth A], O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain F [auth B] Focus chain N [auth A] Focus chain O [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	C [auth B], D [auth B], K [auth A], L [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain K [auth A] Focus chain L [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain P [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain P [auth A]	H [auth B], I [auth B], P [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain P [auth A] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain P [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]