5M9F | pdb_00005m9f

Structure of the two C-terminal domains of bacteriophage K gp144

• PDB DOI: https://doi.org/10.2210/pdb5M9F/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Kayvirus kay
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-01 Released: 2017-12-20 
• Deposition Author(s): Liu, A., Nguyen, T.H., van Raaij, M.J.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal Structure of a Putative Receptor-Binding Protein of Staphylococcus Virus K

Liu, A., Nguyen, T.H., Pichel-Beleiro, A., Coffey, A., van Raaij, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 85.56 kDa 
• Atom Count: 5,523 
• Modeled Residue Count: 634 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF68	A, B, C	262	Kayvirus kay	Mutation(s): 0  Gene Names: PhageK_122
UniProt
Find proteins for Q6Y7P9 (Staphylococcus phage K) Explore Q6Y7P9  Go to UniProtKB:  Q6Y7P9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A], E [auth A], F [auth A], H [auth C], I [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.69	α = 90
b = 81.311	β = 90
c = 154.239	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
autoSHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Liu, A., Nguyen, T.H., van Raaij, M.J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-53425-P

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Data collection, Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations