5CYX | pdb_00005cyx

Crystal Structure of Mouse Protocadherin-24 EC1-3

• PDB DOI: https://doi.org/10.2210/pdb5CYX/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-31 Released: 2016-11-02 
• Deposition Author(s): Johnson, Z.R., Sotomayor, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mouse Protocadherin-24 EC1-3

Johnson, Z.R., Sotomayor, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.31 kDa 
• Atom Count: 2,565 
• Modeled Residue Count: 318 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Cdhr2	A	337	Mus musculus	Mutation(s): 0  Gene Names: Cdhr2
UniProt
Find proteins for E9Q7P9 (Mus musculus) Explore E9Q7P9  Go to UniProtKB:  E9Q7P9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.767	α = 90
b = 74.767	β = 90
c = 140.62	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Johnson, Z.R., Sotomayor, M.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary