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- PDB-5e5v: Structure of amyloid forming peptide NFGAILS (residues 22-28) fro... -

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Basic information

Entry
Database: PDB / ID: 5e5v
TitleStructure of amyloid forming peptide NFGAILS (residues 22-28) from Islet Amyloid Polypeptide
ComponentsNFGAILS (22-28) from islet amyloid polypeptide, synthesized
Keywordsde novo protein / membrane protein / amyloid-like protofibril / Protein Fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.24 Å
AuthorsSoriaga, A.B. / Macdonald, R. / Sawaya, M.R. / Sangwan, S. / 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

Structure viewerMolecule:
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Assembly

Deposited unit
A: NFGAILS (22-28) from islet amyloid polypeptide, synthesized
B: NFGAILS (22-28) from islet amyloid polypeptide, synthesized


Theoretical massNumber of molelcules
Total (without water)1,4422
Polymers1,4422
Non-polymers00
Water1267
1
A: NFGAILS (22-28) from islet amyloid polypeptide, synthesized
B: NFGAILS (22-28) from islet amyloid polypeptide, synthesized
x 6


Theoretical massNumber of molelcules
Total (without water)8,65012
Polymers8,65012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_645x+1,y-1,z1
crystal symmetry operation1_665x+1,y+1,z1
Unit cell
Length a, b, c (Å)8.661, 11.594, 21.552
Angle α, β, γ (deg.)86.39, 82.21, 76.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide NFGAILS (22-28) from islet amyloid polypeptide, synthesized


Mass: 720.815 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.44 Å3/Da / Density % sol: 14.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 7 mg/ml in water and mixed with 10% ethanol and 1.5M 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: Mar 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.24→100 Å / Num. obs: 2283 / % possible obs: 97.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 6.48
Reflection shellResolution: 1.28→1.34 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.6 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.24→21.342 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 206 9.25 %
Rwork0.1728 --
obs0.1759 2227 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→21.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms102 0 0 7 109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008102
X-RAY DIFFRACTIONf_angle_d1.024136
X-RAY DIFFRACTIONf_dihedral_angle_d10.28432
X-RAY DIFFRACTIONf_chiral_restr0.0616
X-RAY DIFFRACTIONf_plane_restr0.00418
LS refinement shellResolution: 1.2403→21.3455 Å
RfactorNum. reflection% reflection
Rfree0.2062 206 -
Rwork0.1728 2021 -
obs--98 %

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