4BGJ | pdb_00004bgj

Crystal structure of the phox-homology domain of human sorting nexin 14

• PDB DOI: https://doi.org/10.2210/pdb4BGJ/pdb

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


• Deposited: 2013-03-27 Released: 2013-05-29 
• Deposition Author(s): Vollmar, M., Kiyani, W., Shrestha, L., Goubin, S., Krojer, T., Pike, A.C.W., Carpenter, E., Quigley, A., McKenzie, A., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.226 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Phox-Homology Domain of Human Sorting Nexin 14

Vollmar, M., Kiyani, W., Shrestha, L., Goubin, S., Krojer, T., Pike, A.C.W., Carpenter, E., Quigley, A., Mckenzie, A., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., 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)

Macromolecule Content 

• Total Structure Weight: 17.4 kDa 
• Atom Count: 960 
• Modeled Residue Count: 118 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SORTING NEXIN-14	A	147	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5W7 (Homo sapiens) Explore Q9Y5W7  Go to UniProtKB:  Q9Y5W7
PHAROS:  Q9Y5W7 GTEx:  ENSG00000135317

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.226 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.611	α = 90
b = 88.611	β = 90
c = 73.082	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Vollmar, M., Kiyani, W., Shrestha, L., Goubin, S., Krojer, T., Pike, A.C.W., Carpenter, E., Quigley, A., McKenzie, A., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Yue, W.W.

Revision History  

• Version 1.0: 2013-05-29
  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