3ZQ8 | pdb_00003zq8

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A monovaccenin LIPID CUBIC PHASE

• PDB DOI: https://doi.org/10.2210/pdb3ZQ8/pdb

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


• Deposited: 2011-06-08 Released: 2012-07-18 
• Deposition Author(s): Hoefer, N., Aragao, D., Caffrey, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystallization of Gramicidin from a Monovaccenin Lipidic Cubic Phase

Hoefer, N., Aragao, D., Caffrey, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 8.6 kDa 
• Atom Count: 633 
• Modeled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MVC	E [auth C], F [auth C], G [auth C]	MONOVACCENIN C21 H40 O4 KJHYUSLWTPMFTN-WHXUGTBJSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.96	α = 90
b = 41.981	β = 107.25
c = 32.429	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: 2012-07-18 
Deposition Author(s): Hoefer, N., Aragao, D., Caffrey, M.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Other
• Version 1.2: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 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
• Version 2.2: 2024-11-13
  Changes: Structure summary