Biological Assembly 1  

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

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

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

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 122.55 kDa 
• Atom Count: 8616 
• Modelled Residue Count: 1026 
• Deposited Residue Count: 1068 
• Unique protein chains: 1

3ABG

X-ray Crystal Analysis of Bilirubin Oxidase from Myrothecium verrucaria at 2.3 angstrom Resolution using a Twin Crystal

• PDB DOI: 10.2210/pdb3ABG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Albifimbria verrucaria
• Mutation(s): No 


• Deposited: 2009-12-10 Released: 2010-08-18 
• Deposition Author(s): Mizutani, K., Toyoda, M., Sagara, K., Takahashi, N., Sato, A., Kamitaka, Y., Tsujimura, S., Nakanishi, Y., Sugiura, T., Yamaguchi, S., Kano, K., Mikami, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 A resolution using a twinned crystal

Mizutani, K., Toyoda, M., Sagara, K., Takahashi, N., Sato, A., Kamitaka, Y., Tsujimura, S., Nakanishi, Y., Sugiura, T., Yamaguchi, S., Kano, K., Mikami, B.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 765-770

• PubMed: 20606269 
• DOI: 10.1107/S1744309110018828
• Primary Citation of Related Structures:  
  3ABG


• PubMed Abstract: 
  

Bilirubin oxidase (BOD), a multicopper oxidase found in Myrothecium verrucaria, catalyzes the oxidation of bilirubin to biliverdin. Oxygen is the electron acceptor and is reduced to water. BOD is used for diagnostic analysis of bilirubin in serum and has attracted considerable attention as an enzymatic catalyst for the cathode of biofuel cells that work under neutral conditions. Here, the crystal structure of BOD is reported for the first time. Blue bipyramid-shaped crystals of BOD obtained in 2-methyl-2,4-pentanediol (MPD) and ammonium sulfate solution were merohedrally twinned in space group P6(3). Structure determination was achieved by the single anomalous diffraction (SAD) method using the anomalous diffraction of Cu atoms and synchrotron radiation and twin refinement was performed in the resolution range 33-2.3 A. The overall organization of BOD is almost the same as that of other multicopper oxidases: the protein is folded into three domains and a total of four copper-binding sites are found in domains 1 and 3. Although the four copper-binding sites were almost identical to those of other multicopper oxidases, the hydrophilic Asn residue (at the same position as a hydrophobic residue such as Leu in other multicopper oxidases) very close to the type I copper might contribute to the characteristically high redox potential of BOD.

---

Organizational Affiliation: 

Laboratory of Applied Structural Biology, Division of Applied Life Sciences, The Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bilirubin oxidase	A, B	534	Albifimbria verrucaria	Mutation(s): 0  EC: 1.3.3.5
UniProt
Find proteins for Q12737 (Albifimbria verrucaria) Explore Q12737  Go to UniProtKB:  Q12737

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	C, E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.742	α = 90
b = 139.742	β = 90
c = 135.561	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-10 
• Released Date: 2010-08-18 
Deposition Author(s): Mizutani, K., Toyoda, M., Sagara, K., Takahashi, N., Sato, A., Kamitaka, Y., Tsujimura, S., Nakanishi, Y., Sugiura, T., Yamaguchi, S., Kano, K., Mikami, B.

Revision History  

• Version 1.0: 2010-08-18
  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, Derived calculations, Non-polymer description, Structure summary