1QV1

Atomic resolution structure of obelin from Obelia longissima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic resolution structure of obelin: soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine.

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

(2003) Biochem Biophys Res Commun 311: 433-439

  • DOI: 10.1016/j.bbrc.2003.09.231
  • Primary Citation of Related Structures:  
    1QV1, 1QV0

  • PubMed Abstract: 
  • The spatial structure of the Ca(2+)-regulated photoprotein obelin has been solved to resolution of 1.1A. Two oxygen atoms are revealed substituted at the C2-position of the coelenterazine in contrast to the obelin structure at 1.73A resolution where ...

    The spatial structure of the Ca(2+)-regulated photoprotein obelin has been solved to resolution of 1.1A. Two oxygen atoms are revealed substituted at the C2-position of the coelenterazine in contrast to the obelin structure at 1.73A resolution where one oxygen atom only was disclosed. The electron density of the second oxygen atom was very weak but after exposing the crystals to a trace of Ca(2+), the electron densities of both oxygen atoms became equally intense. In addition, one Ca(2+) was found bound in the loop of the first EF-hand motif. Four of the ligands were provided by protein residues Asp30, Asn32, Asn34, and the main chain oxygen of Lys36. The other two were from water molecules. From a comparison of B-factors for the residues constituting the active site, it is suggested that the variable electron densities observed in various photoprotein structures could be attributed to different mobilities of the peroxy oxygen atoms.


    Related Citations: 
    • Structure of the Ca2+-regulated photoprotein obelin at 1.7 resolution determined directly from its sulfur substructure
      Liu, Z.-J., Vysotski, E., Chen, C.-J., Rose, J., Lee, J., Wang, B.-C.
      (2000) Protein Sci 9: 2085
    • Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima
      Vysotski, E., Liu, Z.-J., Rose, J., Wang, B.-C., Lee, J.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1965
    • Structural basis for the emission of violet bioluminescence from a W92F obelin mutant
      Deng, L., Vysotski, E., Liu, Z.-J., Markova, S., Malikova, N., Lee, J., Rose, J., Wang, B.-C.
      (2001) FEBS Lett 506: 281
    • Violet Bioluminescence and Fast Kinetics from W92F Obelin: Structure-Based Proposals for the Bioluminescence Triggering and the Identification of the Emitting Species
      Vysotski, E., Liu, Z.-J., Markova, S., Blinks, J., Deng, L., Frank, L., Herko, M., Malikova, N., Rose, J., Wang, B.-C., Lee, J.
      (2003) Biochemistry 42: 6013

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ObelinA195Obelia longissimaMutation(s): 1 
EC: 1.13.12.5
Find proteins for Q27709 (Obelia longissima)
Explore Q27709 
Go to UniProtKB:  Q27709
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZH
Query on CZH

Download CCD File 
A
C2-HYDROPEROXY-COELENTERAZINE
C26 H21 N3 O5
HOSWCJDTHOAORT-SANMLTNESA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.144 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.334α = 90
b = 54.631β = 112.29
c = 52.685γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance