5UJ0 | pdb_00005uj0

Structure of T4Pnkp 3' phosphatase covalently bound to BeF3

• PDB DOI: https://doi.org/10.2210/pdb5UJ0/pdb

• Classification: TRANSFERASE,HYDROLASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-16 Released: 2017-02-08 
• Deposition Author(s): Shuman, S., Chatterjee, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.229 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Truncated T4Pnk covalently bound to BeF3

Shuman, S., Chatterjee, D.

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: 33.67 kDa 
• Atom Count: 2,367 
• Modeled Residue Count: 285 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polynucleotide kinase	A, B	145	Tequatrovirus T4	Mutation(s): 0  Gene Names: pseT EC: 2.7.1.78 (PDB Primary Data), 3.1.3.34 (PDB Primary Data)
UniProt
Find proteins for P06855 (Enterobacteria phage T4) Explore P06855  Go to UniProtKB:  P06855

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BFD	A, B	L-PEPTIDE LINKING	C4 H6 Be F3 N O4		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.229 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.79	α = 90
b = 99.79	β = 90
c = 194.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Shuman, S., Chatterjee, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM63611

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary