3L1R

X-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex with spermidine

• PDB DOI: https://doi.org/10.2210/pdb3L1R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2009-12-14 Released: 2010-12-15 
• Deposition Author(s): Fiorillo, A., Ilari, A., Tavladoraki, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

The crystal structure of the mutant k300m of polyamine oxidase from zea mays unveils the role of lys300 in catalysis

Fiorillo, A., Ilari, A., Tavladoraki, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.7 kDa 
• Atom Count: 7,687 
• Modelled Residue Count: 933 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine oxidase	A, B	478	Zea mays	Mutation(s): 1  Gene Names: PAO EC: 1.5.3 (PDB Primary Data), 1.5.3.14 (UniProt), 1.5.3.15 (UniProt)
UniProt
Find proteins for O64411 (Zea mays) Explore O64411  Go to UniProtKB:  O64411
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SPD	F [auth A], H [auth B]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
SO4	I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.676	α = 90
b = 137.676	β = 90
c = 189.148	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Fiorillo, A., Ilari, A., Tavladoraki, P.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-13
  Changes: Advisory, Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description