1AL4

GRAMICIDIN D FROM BACILLUS BREVIS (N-PROPANOL SOLVATE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  1ALX, 1ALZ

  • 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.


    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
GRAMICIDIN D
A, B
16N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POL
Query on POL

Download SDF File 
Download CCD File 
A, B
N-PROPANOL
1-PROPONOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000152
Query on PRD_000152
A,BGRAMICIDIN DPolypeptide / Antibiotic

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
QIL
Query on QIL
A, B
L-peptide linkingC7 H13 N O3ILE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.434α = 90.00
b = 32.461β = 90.00
c = 24.148γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97model building
SHELXL-97phasing

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