2BE4

X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor.

Bitto, E.Bingman, C.A.Bittova, L.Frederick, R.O.Fox, B.G.Phillips Jr., G.N.

(2009) Proteins 76: 477-483

  • DOI: 10.1002/prot.22362

  • PubMed Abstract: 
  • Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF-hand proteins represent a superfamily of calcium-binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hex ...

    Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF-hand proteins represent a superfamily of calcium-binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hexa-EF-hand protein that is highly expressed in pancreatic islet of Langerhans and neuroendocrine cells and may play a role in the trafficking of secretory granules. We present the X-ray structure of Danio rerio secretagogin, which is 73% identical to human secretagogin, in calcium-free form at 2.1-A resolution. Secretagogin consists of the three globular domains each of which contains a pair of EF-hand motifs. The domains are arranged into a V-shaped molecule with a distinct groove formed at the interface of the domains. Comparison of the secretagogin structure with the solution structure of calcium-loaded calbindin D(28K) revealed a striking difference in the spatial arrangement of their domains, which involves approximately 180 degrees rotation of the first globular domain with respect to the module formed by the remaining domains.


    Organizational Affiliation

    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706-1544, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein LOC449832
A
272Danio rerioGene Names: scgn
Find proteins for Q5XJX1 (Danio rerio)
Go to UniProtKB:  Q5XJX1
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.884α = 90.00
b = 52.748β = 90.00
c = 114.364γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SOLOMONphasing
DENZOdata reduction
ARP/wARPmodel building
SHARPphasing
PHENIXphasing
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2013-02-06
    Type: Database references
  • Version 1.4: 2017-10-18
    Type: Refinement description