3IC4 | pdb_00003ic4

The crystal structure of the glutaredoxin(grx-1) from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb3IC4/pdb

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


• Deposited: 2009-07-17 Released: 2009-08-18 
• Deposition Author(s): Zhang, R., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.239 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

The crystal structure of the glutaredoxin from Archaeoglobus fulgidus

Zhang, R., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, 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)

Macromolecule Content 

• Total Structure Weight: 10.7 kDa 
• Atom Count: 823 
• Modeled Residue Count: 92 
• Deposited Residue Count: 92 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaredoxin (Grx-1)	A	92	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: AF_1536, GI:2649025
UniProt
Find proteins for O28736 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28736  Go to UniProtKB:  O28736

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.239 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.951	α = 90
b = 45.206	β = 90
c = 45.461	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Zhang, R., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary