5XOH

Crystal structure of bergaptol o-methyltransferase complex

• PDB DOI: https://doi.org/10.2210/pdb5XOH/pdb

• Classification: TRANSFERASE
• Organism(s): Kitagawia praeruptora
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-28 Released: 2018-05-23 
• Deposition Author(s): Zhou, Y., Zeng, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Crystal structure of bergaptol o-methyltransferase complex

Zhou, Y., Zeng, Z.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.9 kDa 
• Atom Count: 2,765 
• Modelled Residue Count: 348 
• Deposited Residue Count: 359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bergaptol O-methyltransferase	A	359	Kitagawia praeruptora	Mutation(s): 0  Gene Names: BMT EC: 2.1.1.69
UniProt
Find proteins for A0A166U5H3 (Kitagawia praeruptora) Explore A0A166U5H3  Go to UniProtKB:  A0A166U5H3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
8B6	C [auth A]	4-oxidanylfuro[3,2-g]chromen-7-one C11 H6 O4 GIJHDGJRTUSBJR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.436	α = 90
b = 59.436	β = 90
c = 172.5	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Zhou, Y., Zeng, Z.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references