2WCI | pdb_00002wci

Structure of E. coli monothiol glutaredoxin GRX4 homodimer

PDB DOI: https://doi.org/10.2210/pdb2WCI/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-03-12 Released: 2009-06-23
Deposition Author(s): Iwema, T., Picchiocci, A., Traore, D.A.K., Ferrer, J.-L., Chauvat, F., Jacquamet, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.234 (Depositor), 0.233 (DCC)
R-Value Work:
0.183 (Depositor), 0.185 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis for Delivery of the Intact [Fe2S2] Cluster by Monothiol Glutaredoxin.

Iwema, T., Picciocchi, A., Traore, D.A.K., Ferrer, J.-L., Chauvat, F., Jacquamet, L.

(2009) Biochemistry 48: 6041

PubMed: 19505088 Search on PubMed
DOI: https://doi.org/10.1021/bi900440m
Primary Citation Related Structures:
2WCI

PubMed Abstract:
Glutaredoxins (GRX) are redox proteins which use glutathione as a cofactor and are divided into two classes, monothiol and dithiol. In each class, several GRX have been shown to form [Fe2S2] cluster coordinating homodimers. The dithiol GRX homodimer is proposed to serve as a sequestration form and its iron-sulfur cluster as an oxidative stress sensor. In contrast, the monothiol GRX homodimer has been suggested to act as a scaffold for [Fe2S2] cluster delivery. We present here the structure of a monothiol GRX homodimer (Escherichia coli GRX4) coordinating a [Fe2S2] cluster that reveals the structural basis of intact iron-sulfur cluster delivery.

Organizational Affiliation

Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, 5075 CEA, CNRS, Universite Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France. thomas.iwema@ibs.fr

Macromolecule Content

Total Structure Weight: 30.94 kDa
Atom Count: 1,993
Modeled Residue Count: 225
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAREDOXIN-4	A, B	135	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AC69 (Escherichia coli (strain K12)) Explore P0AC69 Go to UniProtKB: P0AC69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AC69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	D [auth A], F [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.234 (Depositor), 0.233 (DCC)
R-Value Work: 0.183 (Depositor), 0.185 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.3	α = 90
b = 94.3	β = 90
c = 62.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2012-02-29
Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other