Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 87.27 kDa 
• Atom Count: 7341 
• Modelled Residue Count: 737 
• Deposited Residue Count: 747 
• Unique protein chains: 1

1W7C

PPLO at 1.23 Angstroms

• PDB DOI: 10.2210/pdb1W7C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Komagataella pastoris
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2004-09-01 Released: 2006-08-31 
• Deposition Author(s): Duff, A.P., Cohen, A.E., Ellis, P.J., Guss, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.146 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 

Literature

The 1.23 A Structure of Pichia Pastoris Lysyl Oxidase Reveals a Lysine-Lysine Cross-Link

Duff, A.P., Cohen, A.E., Ellis, P.J., Hilmer, K., Langley, D.B., Dooley, D.M., Freeman, H.C., Guss, J.M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1073

• PubMed: 16929109 
• DOI: 10.1107/S0907444906026333
• Primary Citation of Related Structures:  
  1W7C


• PubMed Abstract: 
  

The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Angstrom resolution. PPLO, a copper amine oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor, differs from most other members of the CuAO enzyme family in having the ability to oxidize the side chain of lysine residues in a polypeptide. In the asymmetric unit of the crystals, the structure analysis has located residues 43-779 of the polypeptide chain, seven carbohydrate residues, the active-site Cu atom, an imidazole molecule bound at the active site, two buried Ca(2+) ions, five surface Mg(2+) ions, five surface Cl(-) ions and 1045 water molecules. The crystallographic residuals are R = 0.112 and R(free) = 0.146. The TPQ cofactor and several other active-site residues are poorly ordered, in contrast to the surrounding well ordered structure. A covalent cross-link is observed between two lysine residues, Lys778 and Lys66. The cross-link is likely to have been formed by the oxidation of Lys778 followed by a spontaneous reaction with Lys66. The link is modelled as dehydrolysinonorleucine.

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Organizational Affiliation: 

School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSYL OXIDASE	A	747	Komagataella pastoris	Mutation(s): 0  Gene Names: AOC1, ATY40_BA7504703 EC: 1.4.3.13 (PDB Primary Data), 1.4.3 (UniProt)
UniProt
Find proteins for Q96X16 (Komagataella pastoris) Explore Q96X16  Go to UniProtKB:  Q96X16

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	Q [auth A], R [auth A], S [auth A], T [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IMD	P [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPQ	A	L-PEPTIDE LINKING	C9 H9 N O5		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.146 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.948	α = 90
b = 67.027	β = 118.95
c = 108.688	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-01 
• Released Date: 2006-08-31 
Deposition Author(s): Duff, A.P., Cohen, A.E., Ellis, P.J., Guss, J.M.

Revision History  

• Version 1.0: 2006-08-31
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Advisory, Data collection, Experimental preparation, Other
• Version 1.3: 2019-10-30
  Changes: Data collection, Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary