6LRP

Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with manganese ion

• PDB DOI: https://doi.org/10.2210/pdb6LRP/pdb

• Classification: LYASE
• Organism(s): Chloroflexus aurantiacus J-10-fl
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-16 Released: 2021-07-28 
• Deposition Author(s): Lee, S.H., Kim, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.223 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus

Lee, S.H., Kim, K.J.

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: 48.63 kDa 
• Atom Count: 3,302 
• Modelled Residue Count: 390 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A	436	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0  Gene Names: Caur_3889
UniProt
Find proteins for A9WDE7 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDE7  Go to UniProtKB:  A9WDE7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P3G	C [auth A]	3,6,9,12,15-PENTAOXAHEPTADECANE C12 H26 O5 HYDWALOBQJFOMS-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.223 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.772	α = 90
b = 92.772	β = 90
c = 216.114	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Lee, S.H., Kim, K.J.

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description