Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.94 kDa 
• Atom Count: 2479 
• Modelled Residue Count: 275 
• Deposited Residue Count: 295 
• Unique protein chains: 1

1IYN

Crystal structure of chloroplastic ascorbate peroxidase from tobacco plants and structural insights for its instability

• PDB DOI: 10.2210/pdb1IYN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nicotiana tabacum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-09-03 Released: 2003-09-03 
• Deposition Author(s): Wada, K., Tada, T., Nakamura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Literature

Crystal structure of chloroplastic ascorbate peroxidase from tobacco plants and structural insights into its instability

Wada, K., Tada, T., Nakamura, Y., Ishikawa, T., Yabuta, Y., Yoshimura, K., Shigeoka, S., Nishimura, K.

(2003) J Biochem 134: 239-244

• PubMed: 12966073 
• DOI: 10.1093/jb/mvg136
• Primary Citation of Related Structures:  
  1IYN


• PubMed Abstract: 
  

Ascorbate peroxidase (APX) is a heme-containing protein that plays a central role in scavenging H(2)O(2) in higher plants. The structure of stromal APX (sAPX) was determined at 1.6 A to an R-factor of 19.1% and an R-free-factor of 22.3%. The electrostatic potential of the gamma-channel that connects the molecular surface of sAPX to the gamma-edge of heme was more positive than that of cytosolic APX (cAPX) from pea, so sAPX might bind more easily with ascorbate than cAPX. The overall structure of sAPX was similar to those of cAPX from pea and cytochrome c peroxidase (CCP) from yeast, with a substantial difference in a loop structure located in the vicinity of the heme. The side chain of Arg169 in sAPX corresponding to His169 in cAPX and His181 in CCP extended in the opposite direction from the heme, forming two hydrogen bonds with carbonyl groups in the loop structure. The rapid inactivation of sAPX might be due to the characteristic conformation of Arg169 owing to the loop structure of sAPX.

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Organizational Affiliation: 

Research Institute for Advanced Science and Technology, Osaka Prefecture University, Gakuen-cho 1-2, Sakai, Osaka 599-8570.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloroplastic ascorbate peroxidase	A	295	Nicotiana tabacum	Mutation(s): 0  Gene Names: sapx EC: 1.11.1.11
UniProt
Find proteins for Q8LNY5 (Nicotiana tabacum) Explore Q8LNY5  Go to UniProtKB:  Q8LNY5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.188	α = 90
b = 76.79	β = 90
c = 98.776	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-03 
• Released Date: 2003-09-03 
Deposition Author(s): Wada, K., Tada, T., Nakamura, Y.

Revision History  

• Version 1.0: 2003-09-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance