2QYO

Crystal structure of isoflavone O-methyltransferase homolog in complex with biochanin A and SAH

• PDB DOI: https://doi.org/10.2210/pdb2QYO/pdb

• Classification: TRANSFERASE
• Organism(s): Medicago truncatula
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-15 Released: 2008-08-26 
• Deposition Author(s): Wang, C., Yu, X.-H., Liu, C.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.245 
• R-Value Work: 0.214 

Starting Model: experimental

Literature

Crystal structures of Medicago truncatula isoflavone O-methyltransferase reveal conserved surface binding motifs critical for enzymatic activity

Wang, C., Yu, X.-H., Liu, C.-J.

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)

Macromolecule Content

• Total Structure Weight: 82.36 kDa 
• Atom Count: 5,869 
• Modelled Residue Count: 705 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase	A, B	357	Medicago truncatula	Mutation(s): 0  Gene Names: Medicago truncatula IOMT3 gene EC: 2.1.1.46 (PDB Primary Data), 2.1.1.150 (UniProt)
UniProt
Find proteins for Q06YR3 (Medicago truncatula) Explore Q06YR3  Go to UniProtKB:  Q06YR3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	K [auth A], R [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
QSO	L [auth A], S [auth B]	5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one C16 H12 O5 WUADCCWRTIWANL-UHFFFAOYSA-N
K	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.245 
• R-Value Work: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.54	α = 90
b = 82.049	β = 101.94
c = 101.034	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Wang, C., Yu, X.-H., Liu, C.-J.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description