1K39

The structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA

• PDB DOI: https://doi.org/10.2210/pdb1K39/pdb

• Classification: ISOMERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-10-02 Released: 2003-08-05 
• Deposition Author(s): Mursula, A.M., Geerlof, A., Hiltunen, J.K., Wierenga, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.262 (Depositor) 
• R-Value Work: 
  0.205 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 98.12 kDa 
• Atom Count: 6,587 
• Modelled Residue Count: 806 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
d3,d2-enoyl CoA isomerase ECI1	A, B, C	280	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: ECI1 EC: 5.3.3.8
UniProt
Find proteins for Q05871 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05871  Go to UniProtKB:  Q05871

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO8	F [auth A], G [auth B], I [auth C]	OCTANOYL-COENZYME A C29 H50 N7 O17 P3 S KQMZYOXOBSXMII-CECATXLMSA-N
PO4	D [auth A], E [auth A], H [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.205 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.65	α = 90
b = 116.65	β = 90
c = 216.78	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-05 
Deposition Author(s): Mursula, A.M., Geerlof, A., Hiltunen, J.K., Wierenga, R.K.

Revision History  

• Version 1.0: 2003-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Advisory, Data collection
• Version 1.4: 2021-10-27
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-08-16
  Changes: Data collection, Refinement description