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

• PDB DOI: https://doi.org/10.2210/pdb4LIX/pdb

• Classification: ISOMERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-04 Released: 2013-10-02 
• Deposition Author(s): Koksal, M., Christianson, D.W.

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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 

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

• PubMed: 24036329 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.51 kDa 
• Atom Count: 6,360 
• Modelled Residue Count: 678 
• Deposited Residue Count: 727 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ent-copalyl diphosphate synthase, chloroplastic	A	727	Arabidopsis thaliana	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG8	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
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

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 = 130.177	α = 90
b = 51.393	β = 90
c = 114.308	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Koksal, M., Christianson, D.W.

Revision History  

• 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
• Version 1.3: 2023-12-06
  Changes: Data collection