3WD8

TypeIII polyketide synthases

• PDB DOI: https://doi.org/10.2210/pdb3WD8/pdb

• Classification: TRANSFERASE
• Organism(s): Citrus x microcarpa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-10 Released: 2013-09-04 
• Deposition Author(s): Mori, T., Shimokawa, Y., Matsui, T., Morita, H., Abe, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Cloning, characterization, and crystal structure analysis of novel type III polyketide synthases from Citrus microcarpa

Mori, T., Shimokawa, Y., Matsui, T., Kinjo, K., Kato, R., Noguchi, H., Sugio, S., Morita, H., Abe, I.

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: 178.14 kDa 
• Atom Count: 12,238 
• Modelled Residue Count: 1,564 
• Deposited Residue Count: 1,620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III polyketide synthase quinolone synthase	A, B, C, D	405	Citrus x microcarpa	Mutation(s): 0
UniProt
Find proteins for U3KRF1 (Citrus x microcarpa) Explore U3KRF1  Go to UniProtKB:  U3KRF1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.724	α = 90
b = 135.912	β = 90.05
c = 107.623	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Mori, T., Shimokawa, Y., Matsui, T., Morita, H., Abe, I.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description