4W80

Tetrameric BAP29 vDED with disulfide bonds in crystal contacts

• PDB DOI: https://doi.org/10.2210/pdb4W80/pdb

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


• Deposited: 2014-08-22 Released: 2014-10-29 
• Deposition Author(s): Quistgaard, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.215 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

A disulfide polymerized protein crystal.

Quistgaard, E.M.

(2014) Chem Commun (Camb) 50: 14995-14997

• PubMed: 25327138 
• DOI: https://doi.org/10.1039/c4cc07326f
• Primary Citation of Related Structures:  
  4W7Y, 4W7Z, 4W80


• PubMed Abstract: 
  

  The vDED coiled coil domain from human BAP29 was crystallized in dimeric and tetrameric forms. For the dimer, a disulfide bond was unexpectedly found to bridge a crystal contact, resulting in complete cross-linking along the c-axis. This indicates that it is in principle possible to design spontaneously polymerizing protein crystals.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-171 77 Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 31.13 kDa 
• Atom Count: 2,049 
• Modelled Residue Count: 245 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell receptor-associated protein 29	A, B, C, D	64	Homo sapiens	Mutation(s): 0  Gene Names: BCAP29, BAP29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHQ4 (Homo sapiens) Explore Q9UHQ4  Go to UniProtKB:  Q9UHQ4
PHAROS:  Q9UHQ4 GTEx:  ENSG00000075790

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.215 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.91	α = 90
b = 117.91	β = 90
c = 168.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Quistgaard, E.M.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description