9F49 | pdb_00009f49

Structure of the bacteriophage K gp155 C-terminal domain, seleno-methionine modified version

• PDB DOI: https://doi.org/10.2210/pdb9F49/pdb

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


• Deposited: 2024-04-26 Released: 2025-05-14 
• 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: 1.62 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 

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.

Macromolecule Content 

• Total Structure Weight: 27.42 kDa 
• Atom Count: 2,106 
• Modeled Residue Count: 234 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GP-PDE domain-containing protein	A [auth AAA]	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3P (Subject of Investigation/LOI)	B [auth AAA]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N
PO4	D [auth AAA], E [auth AAA]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	C [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth AAA]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.397	α = 90
b = 42.861	β = 90
c = 123.646	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
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: 2025-05-14
  Type: Initial release