5E59

Crystal structure of reduced state of a novel disulfide oxidoreductase from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb5E59/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-08 Released: 2016-10-12 
• Deposition Author(s): Bihani, S.C., Panicker, L., Kumar, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.206 
• R-Value Work: 0.157 
• R-Value Observed: 0.160 

Literature

drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases.

Bihani, S.C., Panicker, L., Rajpurohit, Y.S., Misra, H.S., Kumar, V.

(2018) Antioxid Redox Signal 28: 296-310

• PubMed: 28899103 
• DOI: https://doi.org/10.1089/ars.2016.6960
• Primary Citation of Related Structures:  
  5CNW, 5CO3, 5COH, 5E59


• PubMed Abstract: 
  

  Living cells employ thioredoxin and glutaredoxin disulfide oxido-reductases to protect thiol groups in intracellular proteins. FrnE protein of Deinococcus radiodurans (drFrnE) is a disulfide oxido-reductase that is induced in response to Cd ²⁺ exposure and is involved in cadmium and radiation tolerance. The aim of this study is to probe structure, function, and cellular localization of FrnE class of proteins.

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Organizational Affiliation: 

1 Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre , Mumbai, India .

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.68 kDa 
• Atom Count: 2,035 
• Modelled Residue Count: 231 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FrnE protein	A	260	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_0659
UniProt
Find proteins for Q9RWK7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RWK7  Go to UniProtKB:  Q9RWK7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.206 
• R-Value Work: 0.157 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.761	α = 90
b = 62.922	β = 90
c = 86.531	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
CrysalisPro	data processing
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Bihani, S.C., Panicker, L., Kumar, V.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description