1MOG | pdb_00001mog

Crystal structure of H. salinarum dodecin

• PDB DOI: https://doi.org/10.2210/pdb1MOG/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Halobacterium salinarum
• Mutation(s): No 


• Deposited: 2002-09-09 Released: 2003-04-15 
• Deposition Author(s): Bieger, B., Essen, L.-O., Oesterhelt, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.208 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal Structure of Halophilic Dodecin: A Novel, Dodecameric Flavin Binding Protein from Halobacterium salinarum

Bieger, B., Essen, L.-O., Oesterhelt, D.

(2003) Structure 11: 375-385

• PubMed: 12679016 
• DOI: https://doi.org/10.1016/s0969-2126(03)00048-0
• Primary Citation Related Structures: 
  1MOG


• PubMed Abstract: 
  

  A novel, 68 amino acid long flavoprotein called dodecin has been discovered in the proteome of Halobacterium salinarum by inverse structural genomics. The 1.7 A crystal structure of this protein shows a dodecameric, hollow sphere-like arrangement of the protein subunits. Unlike other known flavoproteins, which bind only monomeric flavin cofactors, the structure of the dodecin oligomer comprises six riboflavin dimers. The dimerization of these riboflavins along the re-faces is mediated by aromatic, antiparallel pi staggering of their isoalloxazine moieties. A unique aromatic tetrade is formed by further sandwiching of the riboflavin dimers between the indole groups of two symmetry-related Trp36s. So far, the dodecins represent the smallest known flavoproteins. Based on the structure and the wide spread occurrences in pathogenic and soil eubacteria, a function in flavin storage or protection against radical or oxygenic stress is suggested for the dodecins.

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Organizational Affiliation: 
• Department of Membrane Biochemistry, Max Planck Institute for Biochemistry, Am Klopferspitz 18a, D-82152, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 7.83 kDa 
• Atom Count: 645 
• Modeled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dodecin	A	67	Halobacterium salinarum	Mutation(s): 0
UniProt
Find proteins for Q9HPW4 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore Q9HPW4  Go to UniProtKB:  Q9HPW4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBF	G [auth A]	RIBOFLAVIN C17 H20 N4 O6 AUNGANRZJHBGPY-SCRDCRAPSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.208 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.89	α = 90
b = 141.89	β = 90
c = 141.89	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-15 
Deposition Author(s): Bieger, B., Essen, L.-O., Oesterhelt, D.

Revision History  

• Version 1.0: 2003-04-15
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations