2XDC

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

• PDB DOI: https://doi.org/10.2210/pdb2XDC/pdb

• Classification: ANTIBIOTIC
• Organism(s): Brevibacillus brevis
• Mutation(s): No 


• Deposited: 2010-04-30 Released: 2010-08-11 
• Deposition Author(s): Hoefer, N., Aragao, D., Caffrey, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.214 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystallizing Transmembrane Peptides in Lipidic Mesophases

Hoefer, N., Aragao, D., Caffrey, M.

(2010) Biophys J 99: 23

• PubMed: 20682243 
• DOI: https://doi.org/10.1016/j.bpj.2010.05.011
• Primary Citation of Related Structures:  
  2XDC


• 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 small protein targets having

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.44 kDa 
• Atom Count: 935 
• Modelled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GRAMICIDIN A	A, B, C, D, E, F	16	Brevibacillus brevis	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	G [auth A], H [auth A], J [auth B], K [auth C]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FVA	A, B, C, D, E, F	L-PEPTIDE LINKING	C6 H11 N O3		VAL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000150	A, B, C, D, E, F	GRAMICIDIN A	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.214 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.5	α = 90
b = 62.56	β = 99.97
c = 30.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Hoefer, N., Aragao, D., Caffrey, M.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2012-08-29
  Changes: Database references, Refinement description
• Version 1.3: 2012-11-30
  Changes: Other
• Version 1.4: 2019-03-06
  Changes: Advisory, Data collection, Derived calculations, Experimental preparation, Other
• Version 1.5: 2023-03-29
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-02-07
  Changes: Refinement description