2XDC

Structure of linear gramicidin D obtained using Type I crystals grown in a lipid cubic phase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystallizing Transmembrane Peptides in Lipidic Mesophases

Hoefer, N.Aragao, D.Caffrey, M.

(2010) Biophys.J. 99: 23

  • DOI: 10.1016/j.bpj.2010.05.011

  • PubMed Abstract: 
  • Structure determination of membrane proteins by crystallographic means has been facilitated by crystallization in lipidic mesophases. It has been suggested, however, that this so-called in meso method, as originally implemented, would not apply to sm ...

    Structure determination of membrane proteins by crystallographic means has been facilitated by crystallization in lipidic mesophases. It has been suggested, however, that this so-called in meso method, as originally implemented, would not apply to small protein targets having


    Organizational Affiliation

    Membrane Structural and Functional Biology Group, School of Biochemistry and Immunology, and School of Medicine, Trinity College, Dublin, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
A, B, C
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000150
Query on PRD_000150
A,B,C,D,E,FGRAMICIDIN APolypeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 30.500α = 90.00
b = 62.560β = 99.97
c = 30.530γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-08-29
    Type: Database references, Refinement description
  • Version 1.3: 2012-11-30
    Type: Other
  • Version 1.4: 2019-03-06
    Type: Advisory, Data collection, Derived calculations, Experimental preparation, Other