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- PDB-1amt: Crystal structure of alamethicin at 1.5 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 1amt
TitleCrystal structure of alamethicin at 1.5 angstrom resolution
ComponentsALAMETHICIN F30
KeywordsANTIBIOTIC / ALAMETHICIN / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL
Function / homologyAlamethicin / ACETONITRILE / METHANOL / :
Function and homology information
Biological speciesTRICHODERMA VIRIDE (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsFox, R.O. / Richards, F.M.
Citation
Journal: Nature / Year: 1982
Title: A Voltage-Gated Ion Channel Model Inferred from the Crystal Structure of Alamethicin at 1.5-A Resolution.
Authors: Fox Jr, R.O. / Richards, F.M.
#1: Journal: Thesis, Yale
Title: The Crystal Structure of Alamethicin at 1.5 Angstroms Resolution
Authors: Fox, R.O.
History
DepositionDec 8, 1987Processing site: BNL
Revision 1.0Oct 9, 1988Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 1, 2017Group: Derived calculations / Other / Category: pdbx_database_status / pdbx_struct_assembly
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.method_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALAMETHICIN F30
B: ALAMETHICIN F30
C: ALAMETHICIN F30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,34418
Polymers5,8453
Non-polymers49915
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-22 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.330, 29.620, 23.200
Angle α, β, γ (deg.)90.00, 120.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ALAMETHICIN F30 / ALAMETHICIN


Type: Peptaibol / Class: Antibiotic / Mass: 1948.310 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: ALAMETHICIN F30 IS AN EICOSAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (synth.) TRICHODERMA VIRIDE (fungus) / References: NOR: NOR00010, Alamethicin
#2: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#3: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH4O
Compound detailsALAMETHICIN F30 IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...ALAMETHICIN F30 IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, ALAMETHICIN F30 IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 28.2 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-ID
1acetonitrile1
2methanol1

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.5→10 Å /
RfactorNum. reflection
obs0.155 5458
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms417 0 32 0 449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.04
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 5458 / Rfactor obs: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2

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