1ALX

GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.168 
  • R-Value Observed: 0.100 

wwPDB Validation   3D Report Full Report


This is version 1.6 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:  
    1AL4, 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 demonstrate the unexpected presence of stable left-handed antiparallel double-helical heterodimers that vary with the crystallization solvent ...

    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: 
    • Monoclinic Uncomplexed Double-Stranded, Antiparallel, Left-Handed Beta 5.6-Helix (Increases Decreases Beta 5.6) Structure of Gramicidin A: Alternate Patterns of Helical Association and Deformation
      Langs, D.A., Smith, G.D., Courseille, C., Precigoux, G., Hospital, M.
      (1991) Proc Natl Acad Sci U S A 88: 5345

    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 LengthOrganismDetailsImage
GRAMICIDIN AA16Brevibacillus brevisMutation(s): 1 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GRAMICIDIN AB16Brevibacillus brevisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOH
Query on MOH

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FVA
Query on FVA
AL-PEPTIDE LINKINGC6 H11 N O3VAL
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000152
Query on PRD_000152
AGRAMICIDIN DPolypeptide / Antibiotic Ligand Interaction
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000152
Query on PRD_000152
BGRAMICIDIN DPolypeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.168 
  • R-Value Observed: 0.100 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 14.907α = 90
b = 26.014β = 92.03
c = 31.911γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
ENRAF-NONIUSdata reduction
SHELXL-97phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2013-02-06
    Changes: Derived calculations
  • Version 1.6: 2018-04-18
    Changes: Data collection, Other