7CMY | pdb_00007cmy

Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate

• PDB DOI: https://doi.org/10.2210/pdb7CMY/pdb

• Classification: LYASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-07-29 Released: 2021-08-04 
• Deposition Author(s): Kim, K., Ki, D., Lee, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate

Kim, K., Ki, D., Lee, S.H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 96.39 kDa 
• Atom Count: 6,675 
• Modeled Residue Count: 832 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A [auth C], B [auth A]	433	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_1128 EC: 4.1.3.1
UniProt
Find proteins for Q81GQ9 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81GQ9  Go to UniProtKB:  Q81GQ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	D [auth C], G [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
GLV (Subject of Investigation/LOI)	E [auth C], H [auth A]	GLYOXYLIC ACID C2 H2 O3 HHLFWLYXYJOTON-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C, F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.91	α = 90
b = 94.91	β = 90
c = 196.156	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Kim, K., Ki, D., Lee, S.H.

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description