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: 1.55 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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This is version 1.2 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: https://doi.org/10.1016/j.bbagen.2013.09.004
  • Primary Citation of Related Structures:  
    4LIX

  • 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-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ent-copalyl diphosphate synthase, chloroplastic727Arabidopsis thalianaMutation(s): 0 
Gene Names: ABC33, At4g02780, CPS, CPS1, GA1, T5J8.9, TPSGA1
EC: 5.5.1.13
UniProt
Find proteins for Q38802 (Arabidopsis thaliana)
Explore Q38802 
Go to UniProtKB:  Q38802
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38802
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG8
Query on AG8
Download Ideal Coordinates CCD File 
B [auth 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
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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: 1.55 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.177α = 90
b = 51.393β = 90
c = 114.308γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description