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- PDB-5e61: Structure of amyloid-forming peptide FGAILSS (residues 23-29) fro... -

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Basic information

Entry
Database: PDB / ID: 5.0E+61
TitleStructure of amyloid-forming peptide FGAILSS (residues 23-29) from islet amyloid polypeptide
ComponentsFGAILSS (residues 23-29) from islet amyloid polypeptide
Keywordsde novo protein / membrane protein / amyloid-like protofibril / Protein Fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSoriaga, A.B. / Eisenberg, D.
CitationJournal: J.Phys.Chem.B / Year: 2016
Title: Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets.
Authors: Soriaga, A.B. / Sangwan, S. / Macdonald, R. / Sawaya, M.R. / Eisenberg, D.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_ref_seq
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FGAILSS (residues 23-29) from islet amyloid polypeptide
B: FGAILSS (residues 23-29) from islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)1,3882
Polymers1,3882
Non-polymers00
Water00
1
A: FGAILSS (residues 23-29) from islet amyloid polypeptide
x 5
B: FGAILSS (residues 23-29) from islet amyloid polypeptide
x 6


Theoretical massNumber of molelcules
Total (without water)7,63211
Polymers7,63211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation1_545x,y-1,z2
crystal symmetry operation1_565x,y+1,z2
crystal symmetry operation1_655x+1,y,z2
crystal symmetry operation1_645x+1,y-1,z2
crystal symmetry operation1_665x+1,y+1,z1
Unit cell
Length a, b, c (Å)8.770, 9.500, 24.740
Angle α, β, γ (deg.)88.22, 80.00, 70.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide FGAILSS (residues 23-29) from islet amyloid polypeptide


Mass: 693.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.38 Å3/Da / Density % sol: 10.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6.4mg/ml in 20mM Lithium hydroxide and mixed with 0.1M HEPES pH 6.5 and 0.5M Sodium Formate

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→4.38 Å / Num. obs: 647 / % possible obs: 93.36 % / Redundancy: 5.217 % / Rmerge(I) obs: 0.241 / Net I/σ(I): 4.29
Reflection shellResolution: 1.79→1.96 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.4 / % possible all: 72.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→4.38 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.8 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21833 65 10 %RANDOM
Rwork0.16661 ---
obs0.17221 582 93.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.919 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.39 Å20.41 Å2
2---0.6 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.79→4.38 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms98 0 0 0 98
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0297
X-RAY DIFFRACTIONr_angle_refined_deg22.022130
X-RAY DIFFRACTIONr_angle_other_deg0.7643221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.168512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.404202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4851514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0222
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4871.95854
X-RAY DIFFRACTIONr_mcbond_other3.8971.84753
X-RAY DIFFRACTIONr_mcangle_it8.2682.75664
X-RAY DIFFRACTIONr_mcangle_other8.4452.83165
X-RAY DIFFRACTIONr_scbond_it4.9112.67844
X-RAY DIFFRACTIONr_scbond_other4.3052.57943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0833.81866
X-RAY DIFFRACTIONr_long_range_B_refined11.717.89491
X-RAY DIFFRACTIONr_long_range_B_other11.97718.33992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.788→1.835 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 2 -
Rwork0.331 22 -
obs--52.17 %

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