7DKP | pdb_00007dkp

Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7DKP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-25 Released: 2021-12-08 
• Deposition Author(s): Sreekumar, S.N., Arockiasamy, A.
• Funding Organization(s): Department of Biotechnology (DBT, India)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution

Sreekumar, S.N., Arockiasamy, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.33 kDa 
• Atom Count: 8,339 
• Modeled Residue Count: 860 
• Deposited Residue Count: 860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaredoxin	A, B, C, D	215	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AC59 (Escherichia coli (strain K12)) Explore P0AC59  Go to UniProtKB:  P0AC59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], J [auth D]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
FLC	F [auth A], H [auth B], K [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	E [auth A], G [auth B], I [auth C], J [auth D]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37DKP

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.84	α = 90
b = 169.451	β = 93.51
c = 49.842	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Sreekumar, S.N., Arockiasamy, A.

---

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR28766/BRB/10/1701/2018
Department of Biotechnology (DBT, India)	India	BT/PR28080/BID/7/836/2018

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description