4Q37

Crystal structure of the hypothetical protein TM0182 Thermotoga maritima, N-terminal domain.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolutionary relationship of two ancient protein superfolds.

Farias-Rico, J.A.Schmidt, S.Hocker, B.

(2014) Nat.Chem.Biol. 10: 710-715

  • DOI: 10.1038/nchembio.1579

  • PubMed Abstract: 
  • Proteins are the molecular machines of the cell that fold into specific three-dimensional structures to fulfill their functions. To improve our understanding of how the structure and function of proteins arises, it is crucial to understand how evolut ...

    Proteins are the molecular machines of the cell that fold into specific three-dimensional structures to fulfill their functions. To improve our understanding of how the structure and function of proteins arises, it is crucial to understand how evolution has generated the structural diversity we observe today. Classically, proteins that adopt different folds are considered to be nonhomologous. However, using state-of-the-art tools for homology detection, we found evidence of homology between proteins of two ancient and highly populated protein folds, the (βα)8-barrel and the flavodoxin-like fold. We detected a family of sequences that show intermediate features between both folds and determined what is to our knowledge the first representative crystal structure of one of its members, giving new insights into the evolutionary link of two of the earliest folds. Our findings contribute to an emergent vision where protein superfolds share common ancestry and encourage further approaches to complete the mapping of structure space onto sequence space.


    Organizational Affiliation

    Max Planck Institute for Developmental Biology, Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Radical SAM protein
A, B, C, D, E, F
128Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Find proteins for Q9WY26 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WY26
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download SDF File 
Download CCD File 
E, F
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 102.050α = 90.00
b = 145.300β = 90.00
c = 141.710γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
SHELXphasing
PHENIXrefinement
SHELXmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-27
    Type: Database references
  • Version 1.2: 2014-09-03
    Type: Database references