3N3Y | pdb_00003n3y

Crystal structure of Thymidylate Synthase X (ThyX) from Helicobacter pylori with FAD and dUMP at 2.31A resolution

• PDB DOI: https://doi.org/10.2210/pdb3N3Y/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori SS1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-21 Released: 2011-05-25 
• Deposition Author(s): Wang, K., Wang, Q., Chen, J., Chen, L., Jiang, H., Shen, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Structure, Enzymatic Characterization and Inhibitor Discovery of Thymidylate Synthase X (ThyX) from Helicobacter pylori Strain SS1

Wang, K., Wang, Q., Chen, J., Chen, L., Jiang, H., Shen, X.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.17 kDa 
• Atom Count: 7,255 
• Modeled Residue Count: 834 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase thyX	A, B, C, D	216	Helicobacter pylori SS1	Mutation(s): 0  Gene Names: ThyX EC: 2.1.1.148
UniProt
Find proteins for Q5UVJ4 (Helicobacter pylori) Explore Q5UVJ4  Go to UniProtKB:  Q5UVJ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A], I [auth B], K [auth C], M [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UMP	E [auth A], G [auth B], H [auth B], J [auth C], L [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.525	α = 90
b = 79.956	β = 103.14
c = 96.405	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Wang, K., Wang, Q., Chen, J., Chen, L., Jiang, H., Shen, X.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations