6PGY | pdb_00006pgy

MTSL labelled T4 lysozyme pseudo-wild type K65C mutant

• PDB DOI: https://doi.org/10.2210/pdb6PGY/pdb

• Classification: HYDROLASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-06-25 Released: 2020-07-01 
• Deposition Author(s): Cuneo, M.J., Myles, D.A., Li, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Making hydrogens stand out: Enhanced neutron diffraction from biological crystals using dynamic nuclear polarization

Pierce, J., Myles, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 19.09 kDa 
• Atom Count: 1,443 
• Modeled Residue Count: 162 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin	A	164	Tequatrovirus T4	Mutation(s): 3  Gene Names: e, T4Tp126 EC: 3.2.1.17
UniProt
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTN (Subject of Investigation/LOI)	D [auth A]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C10 H18 N O3 S2 MXZPGYFBZHBAQM-UHFFFAOYSA-N
HED	E [auth A]	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.02	α = 90
b = 61.02	β = 90
c = 96.481	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Cuneo, M.J., Myles, D.A., Li, L.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary