1XET | pdb_00001xet

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

• PDB DOI: https://doi.org/10.2210/pdb1XET/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: 2.00 Å
• R-Value Free: 
  0.223 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

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: 181.29 kDa 
• Atom Count: 12,508 
• Modeled Residue Count: 1,540 
• 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  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MCA	H [auth D]	METHYLMALONYL-COENZYME A C25 H40 N7 O19 P3 S MZFOKIKEPGUZEN-AGCMQPJKSA-N
3IO	E [auth B], F [auth C], G [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: 2.00 Å
• R-Value Free:  0.223 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.465	α = 90
b = 111.19	β = 93.13
c = 132.015	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	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: Advisory, Data collection, Refinement description
• Version 1.4: 2024-02-14
  Changes: Advisory, Data collection, Database references, Derived calculations