4B4D

Crystal structure of FAD-containing ferredoxin-NADP reductase from Xanthomonas axonopodis pv. citri

• PDB DOI: https://doi.org/10.2210/pdb4B4D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Xanthomonas citri pv. citri str. 306
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-30 Released: 2013-08-21 
• Deposition Author(s): Martinez-Julvez, M., Orellano, E.G., Tondo, M.L., Hurtado-Guerrero, R., Medina, M., Ceccarelli, E.A., Sanchez-Azqueta, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.230 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Crystal Structure of Fad-Containing Ferredoxin- Nadp Reductase from Xanthomonas Axonopodis Pv. Citri

Tondo, M.L., Hurtado-Guerrero, R., Sanchez-Azqueta, A., Ceccarelli, E.A., Medina, M., Orellano, E.G., Martinez-Julvez, M.

(2013) Biomed Res Int 2013: 06572

• PubMed: 23984418 
• DOI: https://doi.org/10.1155/2013/906572
• Primary Citation of Related Structures:  
  4B4D


• PubMed Abstract: 
  

  We have solved the structure of ferredoxin-NADP(H) reductase, FPR, from the plant pathogen Xanthomonas axonopodis pv. citri, responsible for citrus canker, at a resolution of 1.5 Å. This structure reveals differences in the mobility of specific loops when compared to other FPRs, probably unrelated to the hydride transfer process, which contributes to explaining the structural and functional divergence between the subclass I FPRs. Interactions of the C-terminus of the enzyme with the phosphoadenosine of the cofactor FAD limit its mobility, thus affecting the entrance of nicotinamide into the active site. This structure opens the possibility of rationally designing drugs against the X. axonopodis pv. citri phytopathogen.

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Organizational Affiliation: 

Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario, IBR, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 30.61 kDa 
• Atom Count: 2,363 
• Modelled Residue Count: 256 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERREDOXIN-NADP REDUCTASE	A	262	Xanthomonas citri pv. citri str. 306	Mutation(s): 0  EC: 1.18.1.2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.230 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.699	α = 90
b = 99.775	β = 90
c = 118.785	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Martinez-Julvez, M., Orellano, E.G., Tondo, M.L., Hurtado-Guerrero, R., Medina, M., Ceccarelli, E.A., Sanchez-Azqueta, A.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description