6A1E | pdb_00006a1e

Crystal structure of a synthase 1 from Santalum album in complex with ligand fps

• PDB DOI: https://doi.org/10.2210/pdb6A1E/pdb

• Classification: TRANSFERASE
• Organism(s): Santalum album
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-07 Released: 2019-06-12 
• Deposition Author(s): Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.199 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a synthase 1 from Santalum album in complex with ligand

Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

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: 66.54 kDa 
• Atom Count: 4,678 
• Modeled Residue Count: 512 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sesquisabinene B synthase 1	A	566	Santalum album	Mutation(s): 0
UniProt
Find proteins for A0A0A0RDR2 (Santalum album) Explore A0A0A0RDR2  Go to UniProtKB:  A0A0A0RDR2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPS (Subject of Investigation/LOI)	H [auth A]	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE C15 H28 O6 P2 S MYMLCRQRXFRQGP-YFVJMOTDSA-N
TRS	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3	G [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.199 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.611	α = 90
b = 139.498	β = 90
c = 110.962	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 2.0: 2020-09-02
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description