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- PDB-1pef: PEPTIDE F (EQLLKALEFLLKELLEKL), AMPHIPHILIC OCTADECAPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1pef
TitlePEPTIDE F (EQLLKALEFLLKELLEKL), AMPHIPHILIC OCTADECAPEPTIDE
ComponentsPEPTIDE F (EQLLKALEFLLKELLEKL)
KeywordsSYNTHETIC PROTEIN / ALPHA-HELICAL BUNDLE
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsGaravito, R.M. / Taylor, K. / Yang, N.C.
Citation
Journal: Protein Sci. / Year: 1996
Title: A novel, multilayer structure of a helical peptide.
Authors: Taylor, K.S. / Lou, M.Z. / Chin, T.M. / Yang, N.C. / Garavito, R.M.
#1: Journal: J.Phys.Chem. / Year: 1993
Title: Fluorescence Study of Hexameric Helical Peptide Systems
Authors: Hu, Y. / Chin, T.-M. / Fleming, G.R. / Yang, N.C.
#2: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Self-Assembling Hexameric Helical Bundle Forming Peptides
Authors: Chin, T.-M. / Berndt, K.D. / Yang, N.C.
History
DepositionJun 19, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDE F (EQLLKALEFLLKELLEKL)


Theoretical massNumber of molelcules
Total (without water)2,1741
Polymers2,1741
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.600, 10.670, 29.240
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide PEPTIDE F (EQLLKALEFLLKELLEKL)


Mass: 2173.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.59 Å3/Da / Density % sol: 22.51 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirNa/K2PO4
225 %2-isopropanol1reservoir

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Data collection

Diffraction sourceWavelength: 0.7107
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.41→8 Å / Num. obs: 2360 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Highest resolution: 1.5 Å / % possible obs: 99.5 % / Num. measured all: 18751

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SADNESdata reduction
MADNESdata reduction
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 1.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.196 --
Rwork0.17 --
obs0.17 2360 99.5 %
Displacement parametersBiso mean: 12.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms153 0 0 9 162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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