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- PDB-5e5x: Structure of the amyloid forming peptide ANFLVH (residues 13-18) ... -

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Basic information

Entry
Database: PDB / ID: 5e5x
TitleStructure of the amyloid forming peptide ANFLVH (residues 13-18) from islet amyloid polypeptide
ComponentsANFLVH (residues 13-18) from islet amyloid polypeptide
Keywordsde novo protein / membrane protein / amyloid proto-fibril / Protein Fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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
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

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Structure visualization

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Assembly

Deposited unit
A: ANFLVH (residues 13-18) from islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)7011
Polymers7011
Non-polymers00
Water00
1
A: ANFLVH (residues 13-18) from islet amyloid polypeptide
x 10


Theoretical massNumber of molelcules
Total (without water)7,00810
Polymers7,00810
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_255x-3,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_356x-2,y,z+11
crystal symmetry operation1_456x-1,y,z+11
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_756x+2,y,z+11
Unit cell
Length a, b, c (Å)4.831, 39.726, 9.869
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL UNIT DISPLAYS ONLY A PORTION OF THE CRYSTAL LATTICE TO DEMONSTRATE THE CRYSTAL PACKING CONTENT. THE CRYSTAL PACKING IS FORMED BY A REPETITION IN BOTH DIRECTIONS OF THE PORTION INDICATED IN REMARK 350.

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Components

#1: Protein/peptide ANFLVH (residues 13-18) from islet amyloid polypeptide


Mass: 700.805 Da / Num. of mol.: 1 / 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: 1.31 Å3/Da / Density % sol: 6.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20 mg/ml in water and mixed with 10% (w/v) PEG-8000, 0.1 M Na/K phosphate pH 6.2, and 0.2 M NaCl

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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: Nov 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. obs: 433 / % possible obs: 93.32 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.55
Reflection shellResolution: 1.6→1.72 Å / Mean I/σ(I) obs: 9.7 / % possible all: 87

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Processing

Software
NameClassification
PHENIXrefinement
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→19.863 Å / SU ML: 1.29 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 17.45 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.1612 44 10.16 %
Rwork0.1127 --
obs0.1179 433 93.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6585 Å2-0 Å20.4612 Å2
2---3.0109 Å2-0 Å2
3---2.3524 Å2
Refinement stepCycle: LAST / Resolution: 1.61→19.863 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms50 0 0 0 50
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351
X-RAY DIFFRACTIONf_angle_d0.70469
X-RAY DIFFRACTIONf_dihedral_angle_d16.98815
X-RAY DIFFRACTIONf_chiral_restr0.0588
X-RAY DIFFRACTIONf_plane_restr0.0039
LS refinement shellResolution: 1.6101→19.8645 Å
RfactorNum. reflection% reflection
Rfree0.1612 44 -
Rwork0.1127 389 -
obs--93 %

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