2CJC | pdb_00002cjc

Complexes of Dodecin with Flavin and Flavin-like Ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.222 (Depositor) 
  • R-Value Work: 
    0.194 (Depositor) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Dodecin Sequesters Fad in Closed Conformation from the Aqueous Solution.

Grininger, M.Seiler, F.Zeth, K.Oesterhelt, D.

(2006) J Mol Biology 364: 561

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.083
  • Primary Citation Related Structures: 
    2CIE, 2CIF, 2CJC

  • PubMed Abstract: 

    Both extensive theoretical calculations and experimental data obtained during several decades leave little doubt that flavin adenine dinucleotide (FAD) exists in an open as well as in a closed conformation in aqueous solution. However, the knowledge about the intramolecularly stacked complex of FAD is constructed on indirect methods while direct structural evidence is lacking. Recently, dodecin was reported as an unspecific flavin binding protein which exhibits the unique binding mode of incorporating stacked dimers of flavins into a single binding pocket. Here, we show that FAD is not bound in this manner, but in monomers of intramolecularly stacked conformation. As resulting from the dodecin ligand binding characteristic, this FAD stacked conformation suggests to be directly sequestered from the aqueous solution and thus to be the first X-ray structural view on a FAD solution-stacked form. Moreover, in extraordinary FAD binding, dodecin serves as a model for studying bound monomeric (FAD) versus bound dimeric (e.g. riboflavin) flavin properties.


  • Organizational Affiliation
    • Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 8.43 kDa 
  • Atom Count: 611 
  • Modeled Residue Count: 64 
  • Deposited Residue Count: 68 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VNG1446H68Halobacterium salinarumMutation(s): 0 
UniProt
Find proteins for Q9HPW4 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore Q9HPW4 
Go to UniProtKB:  Q9HPW4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HPW4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.222 (Depositor) 
  • R-Value Work:  0.194 (Depositor) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.04α = 90
b = 142.04β = 90
c = 142.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations