7QLR | pdb_00007qlr

Receptor-binding protein of Clostridium difficile phage CDHS-1

• PDB DOI: https://doi.org/10.2210/pdb7QLR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bacteriophage sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-20 Released: 2022-12-28 
• Deposition Author(s): Wallis, R., Dowah, A., Clokie, M.R.J.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.219 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

The structurome of a Clostridium difficile phage and the remarkable accurate prediction of its novel phage receptor-binding protein

Dowah, A., Wallis, R., Clokie, M.R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 276.92 kDa 
• Atom Count: 19,106 
• Modeled Residue Count: 2,411 
• Deposited Residue Count: 2,464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDHS1_22 Putative tail fiber protein	A, B, C, D	616	Bacteriophage sp.	Mutation(s): 0
UniProt
Find proteins for A0A1J1J928 (Clostridium phage slur17) Explore A0A1J1J928  Go to UniProtKB:  A0A1J1J928

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.219 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.99	α = 90
b = 178.206	β = 90
c = 227.621	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Wallis, R., Dowah, A., Clokie, M.R.J.

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Funding Organization	Location	Grant Number
Other government	Libya	--

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary