9ETJ | pdb_00009etj

Mouse CNPase catalytic domain with nanobody 10E

• PDB DOI: https://doi.org/10.2210/pdb9ETJ/pdb

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


• Deposited: 2024-03-26 Released: 2024-12-11 
• Deposition Author(s): Markusson, S., Raasakka, A., Opazo, F., Kursula, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.304 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Models: experimental

Literature

Mouse CNPase catalytic domain with nanobody 10E

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.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 154.67 kDa 
• Atom Count: 10,494 
• Modeled Residue Count: 1,352 
• Deposited Residue Count: 1,404 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2',3'-cyclic-nucleotide 3'-phosphodiesterase	A, C [auth B], E, G	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: C,D,F,H	B [auth C], D, F, H	131	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth C], J [auth C], K [auth D], L [auth D], M [auth F], N [auth H], O [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.304 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.10868891

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.73	α = 90
b = 118.25	β = 90
c = 122.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	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.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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