9JP6 | pdb_00009jp6

the crystal structure of nuclease encoded by gene PAOP5_157 from Phage PaoP5

• PDB DOI: https://doi.org/10.2210/pdb9JP6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Pseudomonas phage PaoP5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-25 Released: 2025-12-31 
• Deposition Author(s): Wang, C.C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: in silico

Literature

crystal structure of nuclease encoded by gene 157 from Phage PaoP5

Wang, C.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 9.73 kDa 
• Atom Count: 630 
• Modeled Residue Count: 74 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nuclease encoded by gene PAOP5_157	A	83	Pseudomonas phage PaoP5	Mutation(s): 0  Gene Names: PaoP5_157

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.085	α = 90
b = 58.085	β = 90
c = 46.044	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Wang, C.C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release