9ERW | pdb_00009erw

Mouse CNPase catalytic domain with nanobody 8C

• PDB DOI: https://doi.org/10.2210/pdb9ERW/pdb

• Classification: PROTEIN BINDING
• Organism(s): Vicugna pacos, Mus musculus
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.215 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Models: experimental

Literature

Mouse CNPase catalytic domain with nanobody 8C

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

Macromolecule Content 

• Total Structure Weight: 38.25 kDa 
• Atom Count: 2,754 
• Modeled Residue Count: 334 
• Deposited Residue Count: 348 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: E	A [auth E]	128	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2',3'-cyclic-nucleotide 3'-phosphodiesterase	B	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.215 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.10868769

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.86	α = 90
b = 54.17	β = 96.355
c = 80.4	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