6A1D | pdb_00006a1d

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

• PDB DOI: https://doi.org/10.2210/pdb6A1D/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: 1.78 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.169 (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: 65.89 kDa 
• Atom Count: 4,694 
• Modeled Residue Count: 516 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6R2	B [auth A]	[bis(chloranyl)-[oxidanyl-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]phosphoryl]methyl]phosphonic acid C16 H28 Cl2 O6 P2 SCZVAQFGXARGRA-YFVJMOTDSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.437	α = 90
b = 139.487	β = 90
c = 110.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
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 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description