5UJ0

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.229
R-Value Work: 0.184
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Truncated T4Pnk covalently bound to BeF3

Shuman, S., Chatterjee, D.

To be published.

Macromolecule Content

Total Structure Weight: 33.67 kDa
Atom Count: 2,367
Modelled Residue Count: 285
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06855
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BFD Query on 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
R-Value Work: 0.184
R-Value Observed: 0.187
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

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Entry History & Funding Information

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

Shuman, S.

Chatterjee, D.

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

Revision History (Full details and data files)

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

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Help and Resources

5UJ0

Structure of T4Pnkp 3' phosphatase covalently bound to BeF3

Truncated T4Pnk covalently bound to BeF3

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)