3FOG | pdb_00003fog

Crystal structure of the PX domain of sorting nexin-17 (SNX17)

• PDB DOI: https://doi.org/10.2210/pdb3FOG/pdb

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


• Deposited: 2008-12-30 Released: 2009-01-27 
• Deposition Author(s): Wisniewska, M., Tresaugues, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Siponen, M.I., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wikstrom, M., Schueler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the PX domain of sorting nexin-17 (SNX17)

Wisniewska, M., Tresaugues, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Siponen, M.I., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wikstrom, M., Schueler, H.

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: 13.28 kDa 
• Atom Count: 819 
• Modeled Residue Count: 102 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-17	A	115	Homo sapiens	Mutation(s): 0  Gene Names: SNX17, KIAA0064 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q15036 (Homo sapiens) Explore Q15036  Go to UniProtKB:  Q15036
PHAROS:  Q15036 GTEx:  ENSG00000115234

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.89	α = 90
b = 89.89	β = 90
c = 39.26	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Wisniewska, M., Tresaugues, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Siponen, M.I., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wikstrom, M., Schueler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description