4B69

A. fumigatus ornithine hydroxylase (SidA) bound to ornithine

PDB DOI: https://doi.org/10.2210/pdb4B69/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.268
R-Value Work: 0.217
R-Value Observed: 0.220

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/bi301072w
Primary Citation of 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.

Organizational Affiliation

Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, Pavia 27100, Italy.

Macromolecule Content

Total Structure Weight: 58.25 kDa
Atom Count: 3,719
Modelled Residue Count: 448
Deposited Residue Count: 501
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E9QYP0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ORN Query on ORN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	L-ornithine C₅ H₁₂ N₂ O₂ AHLPHDHHMVZTML-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.268
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: I 2 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 77.237	α = 90
b = 84.471	β = 90
c = 145.276	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-03
Type: Initial release
Version 1.1: 2019-09-25
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description