4IRR | pdb_00004irr

Crystal Structure of C.elegans Thymidylate Synthase in Complex with dUMP

• PDB DOI: https://doi.org/10.2210/pdb4IRR/pdb

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


• Deposited: 2013-01-15 Released: 2014-01-29 
• Deposition Author(s): Wilk, P., Dowiercial, A., Banaszak, K., Jarmula, A., Rypniewski, W., Rode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal Structure of C.elegans Thymidylate Synthase in Complex with dUMP

Wilk, P., Dowiercial, A., Banaszak, K., Jarmula, A., Rypniewski, W., Rode, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.95 kDa 
• Atom Count: 5,114 
• Modeled Residue Count: 580 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	315	Caenorhabditis elegans	Mutation(s): 0  EC: 2.1.1.45
UniProt
Find proteins for Q9Y052 (Caenorhabditis elegans) Explore Q9Y052  Go to UniProtKB:  Q9Y052

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	C [auth A], F [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
DTT	D [auth A], E [auth A], G [auth B], H [auth B]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.091	α = 90
b = 135.091	β = 90
c = 155.771	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Wilk, P., Dowiercial, A., Banaszak, K., Jarmula, A., Rypniewski, W., Rode, W.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations