3D2H

Structure of berberine bridge enzyme from Eschscholzia californica, monoclinic crystal form

• PDB DOI: https://doi.org/10.2210/pdb3D2H/pdb

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


• Deposited: 2008-05-08 Released: 2008-10-28 
• Deposition Author(s): Winkler, A., Lyskowski, A., Macheroux, P., Gruber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 62.93 kDa 
• Atom Count: 5,070 
• Modelled Residue Count: 498 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
berberine bridge-forming enzyme	A	538	Eschscholzia californica	Mutation(s): 0  Gene Names: BBE1 EC: 1.21.3.3
UniProt
Find proteins for P30986 (Eschscholzia californica) Explore P30986  Go to UniProtKB:  P30986

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G60005GQ GlyCosmos:  G60005GQ GlyGen:  G60005GQ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSH	E [auth A]	(2R,3S,4S)-5-[(4R)-6',7'-dimethyl-2,3',5-trioxo-1'H-spiro[imidazolidine-4,2'-quinoxalin]-4'(3'H)-yl]-2,3,4-trihydroxypentyl-adenosine diphosphate C27 H35 N9 O16 P2 HUPQKJNMCVRMPP-QUWWARRSSA-N
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.913	α = 90
b = 94.842	β = 100.31
c = 63.977	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Winkler, A., Lyskowski, A., Macheroux, P., Gruber, K.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, 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