8AFJ | pdb_00008afj

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 (Depositor), 0.225 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 394
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 M [auth A] SDF format, chain E [auth B] MOL2 format, chain M [auth A] MOL2 format, chain E [auth B] mmCIF format, chain M [auth A] mmCIF format, chain E [auth B]	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 O [auth A] SDF format, chain N [auth A] SDF format, chain F [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain F [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain F [auth B]	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 L [auth A] SDF format, chain K [auth A] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	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 P [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain P [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain P [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	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] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.228 (Depositor), 0.225 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.276	α = 90
b = 51.845	β = 90.63
c = 78.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-29

Deposition Author(s):

van der Linden, P.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-03-29
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.