2YPS

Crystal structure of the PX domain of human sorting nexin 3

• PDB DOI: https://doi.org/10.2210/pdb2YPS/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-31 Released: 2013-03-20 
• Deposition Author(s): Canning, P., Kiyani, W., Froese, D.S., Krojer, T., Strain-Damerell, C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.255 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Crystal Structure of the Px Domain of Human Sorting Nexin 3

Canning, P., Froese, D.S., Krojer, T., Strain-Damerell, C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.61 kDa 
• Atom Count: 3,102 
• Modelled Residue Count: 408 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SORTING NEXIN-3	A, B, C, D	134	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60493 (Homo sapiens) Explore O60493  Go to UniProtKB:  O60493
PHAROS:  O60493 GTEx:  ENSG00000112335

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.255 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.84	α = 90
b = 81.7	β = 90
c = 184.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Canning, P., Kiyani, W., Froese, D.S., Krojer, T., Strain-Damerell, C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description