7D9L | pdb_00007d9l

Crystal structure of E. coli Grx2: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid

• PDB DOI: https://doi.org/10.2210/pdb7D9L/pdb

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


• Deposited: 2020-10-13 Released: 2021-10-27 
• Deposition Author(s): Sreekumar, S.N., Arockiasamy, A.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E. coli Grx2: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.02 kDa 
• Atom Count: 1,882 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSF (Subject of Investigation/LOI)	F [auth A]	L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE C10 H17 N3 O8 S DMAPAHUEYHXRFI-WDSKDSINSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY (Subject of Investigation/LOI)	G [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37D9L

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.095	α = 90
b = 106.758	β = 90
c = 42.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-27 
Deposition Author(s): Sreekumar, S.N., Arockiasamy, A.

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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: 2021-10-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description