8Z1R | pdb_00008z1r

isocitrate lyase MoMcl1

• PDB DOI: https://doi.org/10.2210/pdb8Z1R/pdb

• Classification: LYASE
• Organism(s): Pyricularia oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-11 Released: 2024-07-03 
• Deposition Author(s): Liu, X.H., Zhao, W.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: in silico

Literature

High-resolution crystal structure of the MoMcl1 protein

Liu, X.H., Zhao, W.H.

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: 123.45 kDa 
• Atom Count: 8,766 
• Modeled Residue Count: 1,024 
• Deposited Residue Count: 1,116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A, B	558	Pyricularia oryzae	Mutation(s): 0  Gene Names: MGCH7_ch7g337
UniProt
Find proteins for G5EH03 (Pyricularia oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)) Explore G5EH03  Go to UniProtKB:  G5EH03

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.43	α = 90
b = 150.495	β = 90
c = 128.243	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Liu, X.H., Zhao, W.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2023YFD1400202-3

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release