6TFN | pdb_00006tfn

Linalool Dehydratase Isomerase in complex with Myrcene

• PDB DOI: https://doi.org/10.2210/pdb6TFN/pdb

• Classification: LYASE
• Organism(s): Castellaniella defragrans 65Phen
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-14 Released: 2020-10-07 
• Deposition Author(s): Cuetos, A., Zukic, E., Danesh-Azari, H.R., Grogan, G.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.209 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms

Cuetos, A., Iglesias-Fernandez, J., Danesh-Azari, H.R., Zukic, E., Dowle, A., Osuna, S., Grogan, G.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c02958

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 420.77 kDa 
• Atom Count: 29,676 
• Modeled Residue Count: 3,626 
• Deposited Residue Count: 3,720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linalool dehydratase-isomerase protein LDI	A, B, C, D, E, F, G, H, I, J	372	Castellaniella defragrans 65Phen	Mutation(s): 0  Gene Names: BN940_14136 EC: 5.4.4.4 (UniProt), 4.2.1.127 (UniProt)
UniProt
Find proteins for E1XUJ2 (Castellaniella defragrans (strain DSM 12143 / CCUG 39792 / 65Phen)) Explore E1XUJ2  Go to UniProtKB:  E1XUJ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N6Q (Subject of Investigation/LOI)	K [auth D], L [auth F], M [auth G], N [auth H], O [auth I], P [auth J]	7-methyl-3-methylidene-oct-1-ene C10 H18 CIGQIEANONTNMS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.209 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.775	α = 90
b = 110.44	β = 99.2
c = 236.485	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Cuetos, A., Zukic, E., Danesh-Azari, H.R., Grogan, G.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P005578/1

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary