6K16

Crystal Structure of Sesquisabinene B Synthase 1 from Santalum album

• PDB DOI: https://doi.org/10.2210/pdb6K16/pdb

• Classification: LYASE
• Organism(s): Santalum album
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-05-09 Released: 2019-06-12 
• Deposition Author(s): Singh, S., Thulasiram, H.V., Kulkarni, K.A.
• Funding Organization(s): Council of Scientific & Industrial Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants

Singh, S., Thulasiram, H.V., Sengupta, D., Kulkarni, K.

(2021) Biochem Biophys Res Commun 536: 107-114

• DOI: https://doi.org/10.1016/j.bbrc.2020.12.041

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.24 kDa 
• Atom Count: 4,140 
• Modelled Residue Count: 506 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sesquisabinene B synthase 1	A	555	Santalum album	Mutation(s): 1
UniProt
Find proteins for A0A0A0RDR2 (Santalum album) Explore A0A0A0RDR2  Go to UniProtKB:  A0A0A0RDR2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.059	α = 90
b = 85.821	β = 97.56
c = 53.399	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Singh, S., Thulasiram, H.V., Kulkarni, K.A.

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Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research	India	BSC0124

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2021-01-13
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description