3BHR | pdb_00003bhr

E. coli TS complexed with 5-NO2dUMP and tetrahydrofolate at 1.9 A resolution (space group 152)

• PDB DOI: https://doi.org/10.2210/pdb3BHR/pdb

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


• Deposited: 2007-11-28 Released: 2008-12-02 
• Deposition Author(s): Roberts, S.A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Structural Studies of Early Events in Catalysis by Thymidylate Synthase

Arendall III, W.B., Hyatt, D.C., Roberts, S.A., Weichsel, A., 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: 31.55 kDa 
• Atom Count: 2,331 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THG	C [auth A]	(6S)-5,6,7,8-TETRAHYDROFOLATE C19 H23 N7 O6 MSTNYGQPCMXVAQ-RYUDHWBXSA-N
NDU	E [auth A]	2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE C9 H14 N3 O10 P ZYBJIJYGXJSDTC-XZBKPIIZSA-N
PO4	B [auth A], D [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: 1.90 Å
• R-Value Free:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.95	α = 90
b = 71.95	β = 90
c = 115.47	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: 2008-12-02 
Deposition Author(s): Roberts, S.A., Montfort, W.R.

Revision History  

• Version 1.0: 2008-12-02
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary