4G14 | pdb_00004g14

Crystal structure of samarosporin I at 293K

• PDB DOI: https://doi.org/10.2210/pdb4G14/pdb

• Classification: ANTIBIOTIC
• Mutation(s): No 


• Deposited: 2012-07-10 Released: 2012-10-03 
• Deposition Author(s): Gessmann, R., Axford, D., Petratos, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free: 
  0.171 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of samarosporin I at atomic resolution.

Gessmann, R., Axford, D., Evans, G., Bruckner, H., Petratos, K.

(2012) J Pept Sci 18: 678-684

• PubMed: 23019149 
• DOI: https://doi.org/10.1002/psc.2454
• Primary Citation Related Structures: 
  4G13, 4G14


• PubMed Abstract: 
  

  The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

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Organizational Affiliation: 
• IMBB-FORTH, N. Plastira 100, Heraklion 70013, Greece.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1.56 kDa 
• Atom Count: 114 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAMAROSPORIN I	A	16	N/A	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
DIV	A	D-PEPTIDE LINKING	C5 H11 N O2		--
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO
PHL	A	L-PEPTIDE LINKING	C9 H13 N O		PHE

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000920	A	SAMAROSPORIN I	Peptaibol / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free:  0.171 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.28	α = 90
b = 9.17	β = 116.59
c = 25.25	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Gessmann, R., Axford, D., Petratos, K.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2012-12-26
  Changes: Database references, Structure summary
• Version 1.3: 2018-07-18
  Changes: Data collection, Database references
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2023-12-06
  Changes: Data collection