1NAR

CRYSTAL STRUCTURE OF NARBONIN REFINED AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.159 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of narbonin at 1.8 A resolution.

Hennig, M.Pfeffer-Hennig, S.Dauter, Z.Wilson, K.S.Schlesier, B.Nong, V.H.

(1995) Acta Crystallogr D Biol Crystallogr 51: 177-189

  • DOI: 10.1107/S0907444994009807
  • Primary Citation of Related Structures:  
    1NAR

  • PubMed Abstract: 
  • The three-dimensional structure of narbonin, a seed protein from Vicia narbonensis L, has been determined at 1.8 A resolution. Phase information was obtained by multiple isomorphous replacement and optimized anomalous dispersion. The narbonin structure was initially traced with only 17% amino-acid sequence information and preliminarily refined to a crystallographic R-factor of 16 ...

    The three-dimensional structure of narbonin, a seed protein from Vicia narbonensis L, has been determined at 1.8 A resolution. Phase information was obtained by multiple isomorphous replacement and optimized anomalous dispersion. The narbonin structure was initially traced with only 17% amino-acid sequence information and preliminarily refined to a crystallographic R-factor of 16.5%. It is now refined to 15.9% using full sequence information derived from cDNA and after the addition of more solvent molecules. The monomeric molecule of narbonin is an eight-stranded parallel beta-barrel surrounded by alpha-helices in a beta/alpha-topology similar to that first observed in triose phosphate isomerase. Differences exist in the N-terminal part of the polypeptide chain, where the first helix is replaced by a loop and the second beta-strand is followed by an additional antiparallel alpha-sheet placed parallel on top of alpha-helices alpha3 and alpha4. Two short additional secondary structures are present. The first, an alpha-helix, is situated between the seventh beta-strand and the following helix, and the second, which is a 3(10) helix, between the eighth strand and the C-terminal helix. The most striking observation is the lack of a known enzymatic function for narbonin, because all TIM-like structures known so far are enzymes.


    Related Citations: 
    • A Tim Barrel Protein without Enzymatic Activity? Crystal Structure of Narbonin at 1.8 Angstroms Resolution
      Hennig, M., Schlesier, B., Dauter, Z., Pfeffer, S., Betzel, C., Hoehne, W.E., Wilson, K.S.
      (1992) FEBS Lett 306: 80
    • Narbonin, a 2S Globulin from Vicia Narbonensis L. Crystallization and Preliminary Crystallographic Data
      Hennig, M., Schlesier, B., Pfeffer, S., Hoehne, W.E.
      (1990) J Mol Biol 215: 339

    Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NARBONINA290Vicia narbonensisMutation(s): 0 
UniProt
Find proteins for Q08884 (Vicia narbonensis)
Explore Q08884 
Go to UniProtKB:  Q08884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08884
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.9α = 90
b = 75.5β = 120.5
c = 50.9γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other