3KPF | pdb_00003kpf

X-ray structure of the mutant Lys300Met of polyamine oxidase from Zea mays

PDB DOI: https://doi.org/10.2210/pdb3KPF/pdb

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

Deposited: 2009-11-16 Released: 2010-11-17
Deposition Author(s): Fiorillo, A., Ilari, A., Tavladoraki, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.223 (Depositor), 0.213 (DCC)
R-Value Work:
0.186 (Depositor), 0.178 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 111.53 kDa
Atom Count: 7,861
Modeled Residue Count: 931
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O64411
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.223 (Depositor), 0.213 (DCC)
R-Value Work: 0.186 (Depositor), 0.178 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.606	α = 90
b = 138.606	β = 90
c = 189.471	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Fiorillo, A.

Ilari, A.

Tavladoraki, P.

Revision History (Full details and data files)

Version 1.0: 2010-11-17
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
Version 2.3: 2024-10-30
Changes: Structure summary