1BDW | pdb_00001bdw

GRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM)

• PDB DOI: https://doi.org/10.2210/pdb1BDW/pdb

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


• Deposited: 1998-05-11 Released: 1998-10-14 
• Deposition Author(s): Burkhart, B.M., Pangborn, W.A., Duax, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.243 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.187 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

The Conducting Form of Gramicidin a is a Right-Handed Double-Stranded Double Helix.

Burkhart, B.M., Li, N., Langs, D.A., Pangborn, W.A., Duax, W.L.

(1998) Proc Natl Acad Sci U S A 95: 12950

• PubMed: 9789021 
• DOI: https://doi.org/10.1073/pnas.95.22.12950
• Primary Citation Related Structures: 
  1AV2, 1BDW


• PubMed Abstract: 
  

  The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDH) reported here agree with 15N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs+ and K+ salts may be in error and that our evidence points to the DSDH as the major conformer responsible for ion transport in membranes.

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Organizational Affiliation: 
• Hauptman-Woodward Medical Research Institute, Inc., 73 High Street, Buffalo, NY 14203, USA. [e-mail]

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)

Macromolecule Content 

• Total Structure Weight: 4.06 kDa 
• Atom Count: 338 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DLE	A, B	D-PEPTIDE LINKING	C6 H13 N O2		--
DVA	A, B	D-PEPTIDE LINKING	C5 H11 N O2		--
FVA	A, B	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	GRAMICIDIN A	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.243 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.187 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 20.584	α = 90
b = 27.905	β = 90
c = 52.04	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Burkhart, B.M., Pangborn, W.A., Duax, W.L.

Revision History  

• Version 1.0: 1998-10-14
  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: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-30
  Changes: Structure summary