5ILD | pdb_00005ild

Tobacco 5-epi-aristolochene synthase with MES buffer molecule and Mg2+ ions

• PDB DOI: https://doi.org/10.2210/pdb5ILD/pdb

• Classification: LYASE
• Organism(s): Nicotiana tabacum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-04 Released: 2017-03-08 
• Deposition Author(s): Koo, H.J., Louie, G.V., Xu, Y., Bowman, M., Noel, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Small-molecule buffer components can directly affect terpene-synthase activity by interacting with the substrate-binding site of the enzyme

Koo, H.J., Louie, G.V., Xu, Y., Bowman, M., Noel, J.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 63.45 kDa 
• Atom Count: 4,581 
• Modeled Residue Count: 536 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-epi-aristolochene synthase	A	550	Nicotiana tabacum	Mutation(s): 0  Gene Names: EAS3, EAS4 EC: 4.2.3.61 (PDB Primary Data), 4.2.3.226 (UniProt), 4.2.3.227 (UniProt)
UniProt
Find proteins for Q40577 (Nicotiana tabacum) Explore Q40577  Go to UniProtKB:  Q40577

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.91	α = 90
b = 126.91	β = 90
c = 123.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Koo, H.J., Louie, G.V., Xu, Y., Bowman, M., Noel, J.P.

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description