4LIX

Crystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in complex with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate at 1.55 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.548 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

1.55 angstrom -resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis.

Koksal, M.Potter, K.Peters, R.J.Christianson, D.W.

(2013) Biochim.Biophys.Acta 1840: 184-190

  • DOI: 10.1016/j.bbagen.2013.09.004

  • PubMed Abstract: 
  • The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeran ...

    The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ent-copalyl diphosphate synthase, chloroplastic
A
727Arabidopsis thalianaMutation(s): 0 
Gene Names: GA1 (ABC33, CPS, CPS1, TPSGA1)
EC: 5.5.1.13
Find proteins for Q38802 (Arabidopsis thaliana)
Go to UniProtKB:  Q38802
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AG8
Query on AG8

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Download CCD File 
A
S-[(2E,6E,10E)-14-(dimethylamino)-3,7,11-trimethyltetradeca-2,6,10-trien-1-yl] trihydrogen thiodiphosphate
C19 H37 N O6 P2 S
WNRLOKILDUQQLN-WNWLUAIZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.548 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 130.177α = 90.00
b = 51.393β = 90.00
c = 114.308γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references