3KGB | pdb_00003kgb

Crystal structure of thymidylate synthase 1/2 from Encephalitozoon cuniculi at 2.2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KGB/pdb

• Classification: TRANSFERASE
• Organism(s): Encephalitozoon cuniculi GB-M1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-28 Released: 2009-11-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thymidylate synthase 1/2 from Encephalitozoon cuniculi at 2.2 A resolution

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Edwards, T.E., Staker, B.

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)

Macromolecule Content 

• Total Structure Weight: 33.19 kDa 
• Atom Count: 2,099 
• Modeled Residue Count: 254 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase 1/2	A	294	Encephalitozoon cuniculi GB-M1	Mutation(s): 0  Gene Names: TS-1, ECU01_0180, TS-2, ECU01_1430 EC: 2.1.1.45
UniProt
Find proteins for O62584 (Encephalitozoon cuniculi (strain GB-M1)) Explore O62584  Go to UniProtKB:  O62584

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KGB

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.63	α = 90
b = 72.28	β = 90
c = 61.68	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description