3FW7 | pdb_00003fw7

Structure of berberine bridge enzyme, H104A variant

• PDB DOI: https://doi.org/10.2210/pdb3FW7/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Eschscholzia californica
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2009-01-17 Released: 2009-05-19 
• Deposition Author(s): Winkler, A., Macheroux, P., Gruber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structural roles of biocovalent flaninylation in berberine bridge enzyme

Winkler, A., Motz, K., Riedl, S., Puhl, M., Macheroux, P., Gruber, K.

To be published.

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: 57.16 kDa 
• Atom Count: 4,678 
• Modeled Residue Count: 498 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reticuline oxidase	A	498	Eschscholzia californica	Mutation(s): 1  Gene Names: BBE1 EC: 1.21.3.3
UniProt
Find proteins for P30986 (Eschscholzia californica) Explore P30986  Go to UniProtKB:  P30986
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-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:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.8	α = 90
b = 68.8	β = 90
c = 247.28	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Winkler, A., Macheroux, P., Gruber, K.

Revision History  

• Version 1.0: 2009-05-19
  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, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-20
  Changes: Structure summary