1ALZ

GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Heterodimer Formation and Crystal Nucleation of Gramicidin D

Burkhart, B.M.Gassman, R.M.Langs, D.A.Pangborn, W.A.Duax, W.L.

(1998) Biophys.J. 75: 2135

  • DOI: 10.1016/S0006-3495(98)77656-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The linear pentadecapeptide antibiotic gramicidin D is a heterogeneous mixture of six components. Precise refinements of three-dimensional structures of naturally occurring gramicidin D in crystals obtained from methanol, ethanol, and n-propanol demo ...

    The linear pentadecapeptide antibiotic gramicidin D is a heterogeneous mixture of six components. Precise refinements of three-dimensional structures of naturally occurring gramicidin D in crystals obtained from methanol, ethanol, and n-propanol demonstrate the unexpected presence of stable left-handed antiparallel double-helical heterodimers that vary with the crystallization solvent. The side chains of Trp residues in the three structures exhibit sequence-specific patterns of conformational preference. Tyr substitution for Trp at position 11 appears to favor beta ribbon formation and stabilization of the antiparallel double helix that acts as a template for gramicidin folding and nucleation of different crystal forms. The fact that a minor component in a heterogeneous mixture influences aggregation and crystal nucleation has potential applications to other systems in which anomalous behavior is exhibited by aggregation of apparently homogeneous materials, such as the enigmatic behavior of prion proteins.


    Related Citations: 
    • Three-Dimensional Structure at 0.86 A of the Uncomplexed Form of the Transmembrane Ion Channel Peptide Gramicidin A.
      Langs, D.A.
      (1988) Science 241: 188


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, Inc., Buffalo, New York 14203-1196, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ILE-GRAMICIDIN C
A
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VAL-GRAMICIDIN A
B
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EOH
Query on EOH

Download SDF File 
Download CCD File 
A, B
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 2 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000153
Query on PRD_000153
AGRAMICIDIN CPolypeptide / Antibiotic

--

PRD_000150
Query on PRD_000150
BGRAMICIDIN APolypeptide / Antibiotic

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.595α = 90.00
b = 32.369β = 90.00
c = 24.219γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97model building
SIEMENSdata scaling
SHELXL-97phasing
SHELXL-97refinement
SIEMENSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other
  • Version 1.5: 2018-04-04
    Type: Data collection, Other