1SL7 | pdb_00001sl7

Crystal structure of calcium-loaded apo-obelin from Obelia longissima

• PDB DOI: https://doi.org/10.2210/pdb1SL7/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Obelia longissima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-05 Released: 2004-12-28 
• Deposition Author(s): Deng, L., Markova, S.V., Vysotski, E.S., Liu, Z.J., Lee, J., Rose, J., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.186 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

All three Ca2+-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin.

Deng, L., Vysotski, E.S., Markova, S.V., Liu, Z.J., Lee, J., Rose, J., Wang, B.C.

(2005) Protein Sci 14: 663-675

• PubMed: 15689515 
• DOI: https://doi.org/10.1110/ps.041142905
• Primary Citation Related Structures: 
  1SL7, 1SL8


• PubMed Abstract: 
  

  The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-protein retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hyroperoxycoelenterazine, and also the same as the Ca2+-discharged obelin bound with product, coleneteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.38 kDa 
• Atom Count: 1,519 
• Modeled Residue Count: 173 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Obelin	A	195	Obelia longissima	Mutation(s): 0
UniProt
Find proteins for Q27709 (Obelia longissima) Explore Q27709  Go to UniProtKB:  Q27709

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.186 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.641	α = 90
b = 58.641	β = 90
c = 110.378	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-28 
Deposition Author(s): Deng, L., Markova, S.V., Vysotski, E.S., Liu, Z.J., Lee, J., Rose, J., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description