4MJB | pdb_00004mjb

Synechocystis sp. PCC 6803 glutaredoxin A-A79S

• PDB DOI: https://doi.org/10.2210/pdb4MJB/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-09-03 Released: 2013-12-04 
• Deposition Author(s): Sutton, R.B., Knaff, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Utility of Synechocystis sp. PCC 6803 glutaredoxin A as a platform to study high-resolution mutagenesis of proteins.

Knaff, D.B., Sutton, R.B.

(2013) Front Plant Sci 4: 461-461

• PubMed: 24298277 
• DOI: https://doi.org/10.3389/fpls.2013.00461
• Primary Citation Related Structures: 
  4MJA, 4MJB, 4MJC, 4MJE


• PubMed Abstract: 
  

  Glutaredoxin from the cyanobacterium Synechocystis sp. PCC 6803 is a small protein, containing only 88 amino acids, that participates in a large number of redox reactions, serving both as an electron donor for enzyme-catalyzed reductions and as a regulator of diverse metabolic pathways. The crystal structures of glutaredoxins from several species have been solved, including the glutaredoxin A isoform from the cyanobacterium Synechocystis sp. PCC 6803. We have utilized the small size of Synechocystis glutaredoxin A and its propensity to form protein crystals that diffract to high resolution to explore a long-standing question in biochemistry; i.e., what are the effects of mutations on protein structure and function? Taking advantage of these properties, we have initiated a long-term educational project that would examine the structural and biochemical changes in glutaredoxin as a function of single-point mutational replacements. Here, we report some of the mutational effects that we have observed to date.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Texas Tech University Lubbock, TX, USA ; Center for Biotechnology and Genomics, Texas Tech University Lubbock, TX, USA.

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: 11.23 kDa 
• Atom Count: 838 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable glutaredoxin ssr2061	A	99	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 1  Gene Names: ssr2061
UniProt
Find proteins for P73492 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73492  Go to UniProtKB:  P73492

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.175	α = 90
b = 38.142	β = 90
c = 51.629	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Sutton, R.B., Knaff, D.B.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2014-04-30
  Changes: Other
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description