6MS8

Crystal Structure of Chalcone Isomerase from Medicago Truncatula Complexed with (2S) Naringenin

• PDB DOI: https://doi.org/10.2210/pdb6MS8/pdb

• Classification: plant protein, isomerase
• Organism(s): Medicago truncatula
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-16 Released: 2019-08-21 
• Deposition Author(s): Burke, J.R., La Clair, J.J., Philippe, R.N., Pabis, A., Jez, J.M., Cortina, G., Kaltenbach, M., Bowman, M.E., Woods, K.B., Nelson, A.T., Tawfik, D.S., Kamerlin, S.C.L., Noel, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases

Burke, J.R., La Clair, J.J., Philippe, R.N., Pabis, A., Jez, J.M., Cortina, G., Kaltenbach, M., Bowman, M.E., Woods, K.B., Nelson, A.T., Tawfik, D.S., Kamerlin, S.C.L., Noel, J.P.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b01926

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 196.26 kDa 
• Atom Count: 13,452 
• Modelled Residue Count: 1,660 
• Deposited Residue Count: 1,792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone-flavonone isomerase family protein	A, B, C, D, E, F, G, H	224	Medicago truncatula	Mutation(s): 0  Gene Names: 11445536, MTR_1g115870
UniProt
Find proteins for B7FJK3 (Medicago truncatula) Explore B7FJK3  Go to UniProtKB:  B7FJK3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAR	I [auth A], J [auth D], K [auth E], L [auth F], M [auth G]	NARINGENIN C15 H12 O5 FTVWIRXFELQLPI-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.09	α = 90
b = 85.09	β = 90
c = 221.508	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Burke, J.R., La Clair, J.J., Philippe, R.N., Pabis, A., Jez, J.M., Cortina, G., Kaltenbach, M., Bowman, M.E., Woods, K.B., Nelson, A.T., Tawfik, D.S., Kamerlin, S.C.L., Noel, J.P.

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references