9Q2Y | pdb_00009q2y

Phosphodiesterase from Burkholderia phage BCSR5 in the open lid conformation

• PDB DOI: https://doi.org/10.2210/pdb9Q2Y/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Burkholderia phage BCSR5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-15 Released: 2025-11-05 
• Deposition Author(s): Doherty, E.E., Blount, N., Doudna, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: in silico

Literature

Phosphodiesterase from Burkholderia phage BCSR5 in the open lid conformation

Doherty, E.E., Blount, N., Doudna, J.A.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.95 kDa 
• Atom Count: 2,795 
• Modeled Residue Count: 320 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CBASS protein Acb1	A, B	165	Burkholderia phage BCSR5	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	C [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.513	α = 90
b = 74.8	β = 90
c = 76.727	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Doherty, E.E., Blount, N., Doudna, J.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)		--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release