5ZTE | pdb_00005zte

Crystal structure of PrxA C119S mutant from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb5ZTE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2018-05-03 Released: 2018-10-10 
• Deposition Author(s): Yang, Y., Cai, W., Wang, J., Pan, W., Liu, L., Wang, M., Zhang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Arabidopsis thaliana peroxiredoxin A C119S mutant.

Yang, Y., Cai, W., Wang, J., Pan, W., Liu, L., Wang, M., Zhang, M.

(2018) Acta Crystallogr F Struct Biol Commun 74: 625-631

• PubMed: 30279313 
• DOI: https://doi.org/10.1107/S2053230X18010920
• Primary Citation Related Structures: 
  5ZTE


• PubMed Abstract: 
  

  Peroxiredoxins (Prxs), a large family of antioxidant enzymes, are abundant in all living organisms. Peroxiredoxin A (PrxA) from Arabidopsis thaliana belongs to the typical 2-Cys Prx family and is localized in the chloroplast. This article reports the crystal structure of a PrxA C119S mutant refined to 2.6 Å resolution. The protein exists as a decamer both in the crystal structure and in solution. The structure is in the reduced state suitable for the approach of peroxide, though conformational changes are needed for the resolving process.

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Organizational Affiliation: 
• School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, People's Republic of China.
Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 229.06 kDa 
• Atom Count: 15,830 
• Modeled Residue Count: 1,939 
• Deposited Residue Count: 2,030 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-Cys peroxiredoxin BAS1, chloroplastic	A, B, C, D, E, F, G, H, I, J	203	Arabidopsis thaliana	Mutation(s): 1  Gene Names: BAS1, At3g11630, F24K9.28, T19F11.3 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for Q96291 (Arabidopsis thaliana) Explore Q96291  Go to UniProtKB:  Q96291

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.212	α = 90
b = 216.189	β = 101.47
c = 98.449	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Yang, Y., Cai, W., Wang, J., Pan, W., Liu, L., Wang, M., Zhang, M.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description