1N21 | pdb_00001n21

(+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3-aza-2,3-dihydrogeranyl diphosphate

• PDB DOI: https://doi.org/10.2210/pdb1N21/pdb

• Classification: ISOMERASE
• Organism(s): Salvia officinalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-21 Released: 2002-11-27 
• Deposition Author(s): Whittington, D.A., Wise, M.L., Urbansky, M., Coates, R.M., Croteau, R.B., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Bornyl diphosphate synthase: Structure and strategy for carbocation manipulation by a terpenoid synthase

Whittington, D.A., Wise, M.L., Urbansky, M., Coates, R.M., Croteau, R.B., Christianson, D.W.

(2002) Proc Natl Acad Sci U S A 99: 15375-15380

• PubMed: 12432096 
• DOI: https://doi.org/10.1073/pnas.232591099
• Primary Citation Related Structures: 
  1N1B, 1N1Z, 1N20, 1N21, 1N22, 1N23, 1N24


• PubMed Abstract: 
  

  The x-ray crystal structure of dimeric (+)-bornyl diphosphate synthase, a metal-requiring monoterpene cyclase from Salvia officinalis, is reported at 2.0-A resolution. Each monomer contains two alpha-helical domains: the C-terminal domain catalyzes the cyclization of geranyl diphosphate, orienting and stabilizing multiple reactive carbocation intermediates; the N-terminal domain has no clearly defined function, although its N terminus caps the active site in the C-terminal domain during catalysis. Structures of complexes with aza analogues of substrate and carbocation intermediates, as well as complexes with pyrophosphate and bornyl diphosphate, provide "snapshots" of the terpene cyclization cascade.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA.

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: 64.42 kDa 
• Atom Count: 4,453 
• Modeled Residue Count: 535 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(+)-bornyl diphosphate synthase	A	549	Salvia officinalis	Mutation(s): 0  EC: 5.5.1.8 (PDB Primary Data), 4.2.3.116 (UniProt), 4.2.3.121 (UniProt)
UniProt
Find proteins for O81192 (Salvia officinalis) Explore O81192  Go to UniProtKB:  O81192

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3AG	E [auth A]	2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE C9 H18 N O7 P2 UWHNDWYDKGVRGE-UHFFFAOYSA-K
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.233 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.38	α = 90
b = 198.38	β = 90
c = 122.84	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-27 
Deposition Author(s): Whittington, D.A., Wise, M.L., Urbansky, M., Coates, R.M., Croteau, R.B., Christianson, D.W.

Revision History  

• Version 1.0: 2002-11-27
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description