3IR4 | pdb_00003ir4

1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione

• PDB DOI: https://doi.org/10.2210/pdb3IR4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-21 Released: 2009-09-01 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Halavaty, A., Dauter, Z., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.116 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Literature

1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione.

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Halavaty, A., Dauter, Z., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 25.73 kDa 
• Atom Count: 2,551 
• Modeled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaredoxin 2	A	218	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: grxB, STM1165
UniProt
Find proteins for Q7CQR3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CQR3  Go to UniProtKB:  Q7CQR3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.116 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33ir4

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.24	α = 90
b = 58.76	β = 90
c = 87.93	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CRANK	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Halavaty, A., Dauter, Z., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2011-12-21
  Changes: Non-polymer description
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary