2BE4

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

• PDB DOI: https://doi.org/10.2210/pdb2BE4/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-21 Released: 2005-11-01 
• Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Han, B.W., Bitto, E., Bingman, C.A., Bae, E., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.253 
• R-Value Work: 0.175 
• R-Value Observed: 0.179 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4U

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

• PubMed: 19241471 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.05 kDa 
• Atom Count: 2,445 
• Modelled Residue Count: 270 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein LOC449832	A	272	Danio rerio	Mutation(s): 10  Gene Names: Dr.36843, BC083168
UniProt
Find proteins for Q5XJX1 (Danio rerio) Explore Q5XJX1  Go to UniProtKB:  Q5XJX1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.253 
• R-Value Work: 0.175 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.884	α = 90
b = 52.748	β = 90
c = 114.364	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
SHELXD	phasing
SOLOMON	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-01 
Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Han, B.W., Bitto, E., Bingman, C.A., Bae, E., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

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