4W80 | pdb_00004w80

Tetrameric BAP29 vDED with disulfide bonds in crystal contacts

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.215 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

A disulfide polymerized protein crystal.

Quistgaard, E.M.

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

  • DOI: https://doi.org/10.1039/c4cc07326f
  • Primary Citation 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.

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

Macromolecule Content 

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

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
B-cell receptor-associated protein 29
A, B, C, D
64Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHQ4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
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 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.91α = 90
b = 117.91β = 90
c = 168.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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