6U0B | pdb_00006u0b

Neutron crystal structure of wtT4LD

• PDB DOI: https://doi.org/10.2210/pdb6U0B/pdb

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


• Deposited: 2019-08-14 Released: 2020-08-19 
• Deposition Author(s): Cuneo, M.J., Myles, D.A., Li, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

---

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Solvent entry into cavities of T4 lysozyme.

Li, L., Myles, D.A., Cuneo, M.J.

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: 18.66 kDa 
• Atom Count: 1,341 
• Modeled Residue Count: 164 
• 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): 2  Gene Names: e, T4Tp126 EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.87	α = 90
b = 60.87	β = 90
c = 97	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Mantid	data reduction
LaueView	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Cuneo, M.J., Myles, D.A., Li, L.

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description