1UNO

Crystal structure of a d,l-alternating peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution and Structure of an Alternating D,L-Peptide

Alexopoulos, E.Kuesel, A.Sheldrick, G.M.Diederichsen, U.Uson, I.

(2004) Acta Crystallogr.,Sect.D 60: 1971

  • DOI: 10.1107/S0907444904022292

  • PubMed Abstract: 
  • The crystal structure of H-(L-Tyr-D-Tyr)(4)-L-Lys-OH has been determined to 1.3 A resolution. The D,L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) A. The ...

    The crystal structure of H-(L-Tyr-D-Tyr)(4)-L-Lys-OH has been determined to 1.3 A resolution. The D,L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) A. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel beta-helix. The structure has been solved by SIRAS using a crystal soaked in an iodide-containing solution for 1 min. The programs SHELXD and SHELXE were used to determine the iodide substructure and also the experimental electron-density map. Using the coordinates of known D,L-peptides deposited in the PDB, several attempts were made to solve the structure by molecular-replacement techniques. Although the backbone of the MR model selected shows great similarity and was used to trace the actual peptide structure in the map, it was not possible to obtain the correct solution before the experimental phases became available. The correct fragment orientations are easily determined, but the same does not apply to the translation search. Nevertheless, insights into fragment search and expansion were gained from the tests described in this paper. The correlation coefficient calculated with the resolution shell of data around 2.4 A, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments.


    Organizational Affiliation

    Lehrstuhl für Strukturchemie, Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-(L-TYR-D-TYR)4-LYS-OH
A, B
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000107
Query on PRD_000107
A,BH-(L-TYR-D-TYR)4-LYS-OHPolypeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.249 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 27.990α = 90.00
b = 27.990β = 90.00
c = 78.930γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
DENZOdata reduction
SHELXL-97refinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-24
    Type: Initial release
  • Version 1.1: 2012-11-30
    Type: Other
  • Version 1.2: 2017-02-08
    Type: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance