6MS8 | pdb_00006ms8

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.241 (Depositor), 0.244 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (DCC)
R-Value Observed:
0.230 (Depositor)

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Ligand Structure Quality Assessment

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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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone-flavonone isomerase family protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7FJK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAR Query on NAR Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth D] SDF format, chain L [auth F] SDF format, chain M [auth G] SDF format, chain K [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth D] MOL2 format, chain L [auth F] MOL2 format, chain M [auth G] MOL2 format, chain K [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth D] mmCIF format, chain L [auth F] mmCIF format, chain M [auth G] mmCIF format, chain K [auth E]	I [auth A], J [auth D], K [auth E], L [auth F], M [auth G]	NARINGENIN C₁₅ H₁₂ O₅ FTVWIRXFELQLPI-ZDUSSCGKSA-N		Interactions Focus chain I [auth A] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Focus chain M [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Focus chain M [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241 (Depositor), 0.244 (DCC)
R-Value Work: 0.228 (Depositor), 0.229 (DCC)
R-Value Observed: 0.230 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Kamerlin, S.C.L.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.