2V18 | pdb_00002v18

Crystal structure of the T. thermophilus dodecin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.244 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The Dodecin from Thermus Thermophilus, a Bifunctional Cofactor Storage Protein.

Meissner, B.Schleicher, E.Weber, S.Essen, L.-O.

(2007) J Biological Chem 282: 33142

  • DOI: https://doi.org/10.1074/jbc.M704951200
  • Primary Citation Related Structures: 
    2UX9, 2V18, 2V19, 2V21

  • PubMed Abstract: 

    Dodecins are so far the smallest known flavoproteins (68-71 amino acids) and are most likely involved in prokaryotic flavin storage. The dodecin monomers adopt a simple betaalphabetabeta-fold and assemble to hollow sphere-like dodecameric complexes. Flavin binding by the dodecin from Thermus thermophilus showed a 1:1 stoichiometry and apparent dissociation constants in the submicromolar to nanomolar range as characterized by isothermal titration calorimetry and fluorescence titrations. The x-ray structures of the flavin-prebound and FMN-reconstituted state of the T. thermophilus dodecin revealed binding of FMN dimers in a novel si-si- rather than the re-re- orientation of their isoalloxazine moieties as found before in an archaeal dodecin. Electron paramagnetic resonance studies demonstrated that upon reduction the excess electron is localized only on one flavin, thus making dodecin-bound flavins highly refractory to redox chemistry. Besides FMN dimers, trimers of coenzyme A are additionally bound to this eubacterial dodecin along the 3-fold symmetry face II of the dodecin complex. Therefore, dodecins can act as bifunctional cofactor storage proteins that sequester catalytic cofactors in prokaryotes very efficiently in an aggregated and unreactive state.


  • Organizational Affiliation
    • Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 103.93 kDa 
  • Atom Count: 7,201 
  • Modeled Residue Count: 816 
  • Deposited Residue Count: 816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DODECIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
68Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SIE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIE3 
Go to UniProtKB:  Q5SIE3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIE3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA

Query on COA



Download:Ideal Coordinates CCD File
BA [auth I]
DA [auth J]
FA [auth K]
O [auth B]
Q [auth C]
BA [auth I],
DA [auth J],
FA [auth K],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
AA [auth I]
CA [auth J]
EA [auth K]
GA [auth L]
M [auth A]
AA [auth I],
CA [auth J],
EA [auth K],
GA [auth L],
M [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.481α = 90
b = 98.038β = 90
c = 137.595γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description