6A2D | pdb_00006a2d

Crystal structure of a synthase 2 from santalum album in complex with ligand1

• PDB DOI: https://doi.org/10.2210/pdb6A2D/pdb

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


• Deposited: 2018-06-10 Released: 2019-06-12 
• Deposition Author(s): Han, X., Ko, T.P., Liu, W.D., Zheng, Y.Y., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a synthase 2 from santalum album

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 132.03 kDa 
• Atom Count: 9,378 
• Modeled Residue Count: 1,029 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sesquisabinene B synthase 2	A, B	566	Santalum album	Mutation(s): 0
UniProt
Find proteins for A0A0A0RCB5 (Santalum album) Explore A0A0A0RCB5  Go to UniProtKB:  A0A0A0RCB5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6R2 (Subject of Investigation/LOI)	C [auth A], F [auth B]	[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
MG	D [auth A], E [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.527	α = 90
b = 132.527	β = 90
c = 141.903	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., Zheng, Y.Y., 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, Other, Refinement description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description