RCSB PDB - 1N20: (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-aza-2,3-dihydrogeranyl diphosphate

 1N20

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Bornyl Diphosphate Synthase: Structure and Strategy for Carbocation Manipulation by a Terpenoid Cyclase

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

  • DOI: https://doi.org/10.1073/pnas.232591099
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(+)-bornyl diphosphate synthase
A, B
549Salvia officinalisMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO81192
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3AG
Query on 3AG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
C9 H18 N O7 P2
UWHNDWYDKGVRGE-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]
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: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.08α = 90
b = 117.54β = 90
c = 120.04γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3AGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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