4MEJ

Crystal structure of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine)

• PDB DOI: https://doi.org/10.2210/pdb4MEJ/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Lactobacillus helveticus H10
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-26 Released: 2014-10-15 
• Deposition Author(s): Paul, D., Seckute, J., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Glycosylation of a tricyclic purine analog at alternative sites by nucleoside 2 -deoxyribosyltransferases

Ye, W., Paul, D., Gao, L., Seckute, J., Sangaiah, R., Karupiah, J., Zhang, Z., Kaminski, A.P., Ealick, S.E., Gold, A., Ball, L.M.

(2014) PLoS One 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 56.92 kDa 
• Atom Count: 4,292 
• Modelled Residue Count: 501 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A, B, C	167	Lactobacillus helveticus H10	Mutation(s): 0  Gene Names: LBHH_1694

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
28Y	E [auth A], F [auth B], G [auth B]	3H-imidazo[2,1-b]purin-4(5H)-one C7 H5 N5 O OSXKHFTZRHDUJN-UHFFFAOYSA-N
SO4	D [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.695	α = 90
b = 79.695	β = 90
c = 186.697	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Paul, D., Seckute, J., Ealick, S.E.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description