4B63 | pdb_00004b63

A. fumigatus ornithine hydroxylase (SidA) bound to NADP and ornithine

• PDB DOI: https://doi.org/10.2210/pdb4B63/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus fumigatus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-08-09 Released: 2012-10-03 
• Deposition Author(s): Franceschini, S., Fedkenheuer, M., Vogelaar, N.J., Robinson, H.H., Sobrado, P., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structural Insight Into the Mechanism of Oxygen Activation and Substrate Selectivity of Flavin-Dependent N-Hydroxylating Monooxygenases.

Franceschini, S., Fedkenheuer, M., Vogelaar, N.J., Robinson, H.H., Sobrado, P., Mattevi, A.

(2012) Biochemistry 51: 7043

• PubMed: 22928747 
• DOI: https://doi.org/10.1021/bi301072w
• Primary Citation Related Structures: 
  4B63, 4B64, 4B65, 4B66, 4B67, 4B68, 4B69


• PubMed Abstract: 
  

  SidA from the human pathogen Aspergillus fumigatus catalyzes the generation of N(5)-hydroxyornithine in the biosynthesis of siderophores, a reaction essential for virulence. The crystal structures of SidA in complex with ornithine and lysine reveal the geometry of the interactions among flavin, NADP(+), and the substrate amine group that underlie the hydroxylation reaction. The structural elucidation of the enzyme in complex with arginine provides insight into the role of electrostatics and hydrogen bonding in the mechanism of oxygen activation in this family of enzymes.

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Organizational Affiliation: 
• Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, Pavia 27100, Italy.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 59.09 kDa 
• Atom Count: 3,921 
• Modeled Residue Count: 451 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ORNITHINE N5 MONOOXYGENASE	A	501	Aspergillus fumigatus	Mutation(s): 0  EC: 1.14.13.196
UniProt
Find proteins for E9QYP0 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore E9QYP0  Go to UniProtKB:  E9QYP0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ORN	D [auth A]	L-ornithine C5 H12 N2 O2 AHLPHDHHMVZTML-BYPYZUCNSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.806	α = 90
b = 84.424	β = 90
c = 145.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Franceschini, S., Fedkenheuer, M., Vogelaar, N.J., Robinson, H.H., Sobrado, P., Mattevi, A.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description