9F5M | pdb_00009f5m

Structure of the C-terminal domain of bacteriophage K gp155, native

• PDB DOI: https://doi.org/10.2210/pdb9F5M/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Staphylococcus phage K
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-29 Released: 2025-04-09 
• Deposition Author(s): Pichel, A., van Raaij, M.J.
• Funding Organization(s): Agencia Estatal de Investigacion (AEI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.213 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Structure of bacteriophage K gp155

Pichel, A., van Raaij, M.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.86 kDa 
• Atom Count: 4,457 
• Modeled Residue Count: 468 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GP-PDE domain-containing protein	A [auth AAA], B [auth BBB]	235	Staphylococcus phage K	Mutation(s): 0  Gene Names: 812_115, 812a_115, 812F1_115, K1/420_115, K1_115 EC: 3.1.4.46
UniProt
Find proteins for A0A410TAW0 (Staphylococcus phage J-Sa36) Explore A0A410TAW0  Go to UniProtKB:  A0A410TAW0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth AAA], E [auth BBB]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	D [auth AAA], F [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.213 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.197 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.13	α = 90
b = 43.334	β = 94.084
c = 98.982	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Pichel, A., van Raaij, M.J.

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Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	BFU2014-53425-P
Agencia Estatal de Investigacion (AEI)	Spain	BFU2017-82207-P
Agencia Estatal de Investigacion (AEI)	Spain	PID2021-125597NB-I00

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release