9ERT | pdb_00009ert

Mouse CNPase catalytic domain with nano body 5E

• PDB DOI: https://doi.org/10.2210/pdb9ERT/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-25 Released: 2024-12-11 
• Deposition Author(s): Markusson, S., Raasakka, A., Opazo, F., Kursula, P.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.323 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.293 (Depositor) 

Starting Models: experimental

Literature

Mouse CNPase catalytic domain with nano body 5E

Markusson, S., Raasakka, A., Opazo, F., Kursula, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 38.51 kDa 
• Atom Count: 2,641 
• Modeled Residue Count: 342 
• Deposited Residue Count: 352 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2',3'-cyclic-nucleotide 3'-phosphodiesterase	A	220	Mus musculus	Mutation(s): 0  Gene Names: Cnp, Cnp1 EC: 3.1.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P16330 (Mus musculus) Explore P16330  Go to UniProtKB:  P16330
IMPC:  MGI:88437

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: B	B	132	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.323 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.293 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.10868256

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.832	α = 90
b = 110.832	β = 90
c = 83.281	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Markusson, S., Raasakka, A., Opazo, F., Kursula, P.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release