1XES | pdb_00001xes

Crystal structure of stilbene synthase from Pinus sylvestris

• PDB DOI: https://doi.org/10.2210/pdb1XES/pdb

• Classification: TRANSFERASE
• Organism(s): Pinus sylvestris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-09-12 Released: 2006-04-11 
• Deposition Author(s): Ng, S.H., Chirgadze, D., Spiteller, D., Li, T.L., Spencer, J.B., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of stilbene synthase from Pinus sylvestris

Ng, S.H., Chirgadze, D., Spiteller, D., Li, T.L., Spencer, J.B., Blundell, T.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 180.63 kDa 
• Atom Count: 12,492 
• Modeled Residue Count: 1,534 
• Deposited Residue Count: 1,652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropinosylvin synthase	A, B, C, D	413	Pinus sylvestris	Mutation(s): 0  Gene Names: STS EC: 2.3.1 (PDB Primary Data), 2.3.1.146 (UniProt)
UniProt
Find proteins for Q02323 (Pinus sylvestris) Explore Q02323  Go to UniProtKB:  Q02323

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3IO	E [auth A], F [auth B], G [auth C], H [auth D]	3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID C11 H9 N O3 RSTKLPZEZYGQPY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.366	α = 90
b = 111.373	β = 93.05
c = 131.695	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Ng, S.H., Chirgadze, D., Spiteller, D., Li, T.L., Spencer, J.B., Blundell, T.L.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description