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- PDB-2bfi: Molecular basis for amyloid fibril formation and stability -

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Basic information

Entry
Database: PDB / ID: 2bfi
TitleMolecular basis for amyloid fibril formation and stability
ComponentsSYNTHETIC PEPTIDE
KeywordsAMYLOID / PI-PI BONDING / BETA-SHEET INTERACTIONS
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.1 Å
AuthorsMakin, O.S. / Atkins, E. / Sikorski, P. / Johansson, J. / Serpell, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Molecular Basis for Amyloid Fibril Formation and Stability
Authors: Sumner Makin, O. / Atkins, E. / Sikorski, P. / Johansson, J. / Serpell, L.C.
History
DepositionDec 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 6, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Source and taxonomy / Version format compliance
Revision 1.2May 8, 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: SYNTHETIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)1,4661
Polymers1,4661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)9.520, 21.300, 48.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIN ORDER TO GENERATE THE SYMMETRY-RELATED OBJECTS DESCRIBEDIN THE ACCOMPANYING PUBLICATION, THE COORDINATES SHOULD BETRANSLATED BY VECTOR (0.45 , -02.14, 1.47) TO GENERATE THECORRECT ORIGIN AND SYMMETRY OPERATIONS APPLIED TO THE NEWCOORDINATES.

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Components

#1: Protein/peptide SYNTHETIC PEPTIDE


Mass: 1465.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.66 Å3/Da / Density % sol: 26.06 %

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1→100 Å / Num. obs: 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CERIUS2refinement
MOSFLMdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 1.1→100 Å
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM FIBER DIFFRACTION DATA.
Refinement stepCycle: LAST / Resolution: 1.1→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms104 0 0 0 104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.039
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.386
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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