4KFF | pdb_00004kff

Crystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 8.5

PDB DOI: https://doi.org/10.2210/pdb4KFF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ogataea angusta
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2013-04-26 Released: 2013-08-28
Deposition Author(s): Johnson, B.J., Yukl, E.T., Klema, V.J., Wilmot, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.185 (Depositor), 0.192 (DCC)
R-Value Work:
0.142 (Depositor), 0.152 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural evidence for the semiquinone in a copper amine oxidase from Hansenula polymorpha: implications for the catalytic mechanism

Johnson, B.J., Yukl, E.T., Klema, V.J., Klinman, J.P., Wilmot, C.M.

(2013) J Biological Chem

Macromolecule Content

Total Structure Weight: 234.46 kDa
Atom Count: 16,993
Modeled Residue Count: 1,970
Deposited Residue Count: 2,076
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal primary amine oxidase	A, B, C	692	Ogataea angusta	Mutation(s): 0 Gene Names: AMO EC: 1.4.3.21
UniProt
Find proteins for P12807 (Pichia angusta) Explore P12807 Go to UniProtKB: P12807
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12807
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A]	D [auth A], L [auth B], P [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain L [auth B] Focus chain P [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYY Query on TYY	A, B, C	L-PEPTIDE LINKING	C₉ H₁₀ N₂ O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.185 (Depositor), 0.192 (DCC)
R-Value Work: 0.142 (Depositor), 0.152 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.022	α = 90
b = 153.316	β = 90
c = 223.048	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-27
Changes: Structure summary