3B9H | pdb_00003b9h

E. coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE

• PDB DOI: https://doi.org/10.2210/pdb3B9H/pdb

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


• Deposited: 2007-11-05 Released: 2008-11-25 
• Deposition Author(s): Roberts, S.A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.233 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structural Studies of Early Events in the Thymidylate Synthase Reaction

Arendall III, W.B., Roberts, S.A., Hyatt, D.C., Dahlgren, A.L., Maley, F., Montfort, W.R.

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: 31.1 kDa 
• Atom Count: 2,241 
• Modeled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	264	Escherichia coli	Mutation(s): 0  Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDU	D [auth A]	2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE C9 H14 N3 O10 P ZYBJIJYGXJSDTC-XZBKPIIZSA-N
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM	A	L-PEPTIDE LINKING	C6 H11 N O4 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.233 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.6	α = 90
b = 71.6	β = 90
c = 115.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MADNESS	data collection
PROCOR	data reduction
PROCOR	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Roberts, S.A., Montfort, W.R.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-04-18
  Changes: Data collection
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary