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- PDB-5e5z: Structure of the amyloid forming peptide LVHSSN (residues -

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Entry
Database: PDB / ID: 5e5z
TitleStructure of the amyloid forming peptide LVHSSN (residues
ComponentsLVHSSN (residues 16-21) 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: 1.664 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

Structure viewerMolecule:
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Assembly

Deposited unit
A: LVHSSN (residues 16-21) from islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)6571
Polymers6571
Non-polymers00
Water181
1
A: LVHSSN (residues 16-21) from islet amyloid polypeptide
x 10


Theoretical massNumber of molelcules
Total (without water)6,56710
Polymers6,56710
Non-polymers00
Water18010
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
crystal symmetry operation2_645-x+1,y-1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_745-x+2,y-1/2,-z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Unit cell
Length a, b, c (Å)9.643, 9.609, 19.029
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide LVHSSN (residues 16-21) from islet amyloid polypeptide


Mass: 656.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.32 Å3/Da / Density % sol: 6.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20 mg/ml in water and mixed with 0.09 M HEPES pH 7.5, 1.26M tri-sodium citrate, and 10% glycerol

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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 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 1136 / % possible obs: 92.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.86

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.664→9.459 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.27 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.1983 18 4.6 %
Rwork0.1673 --
obs0.1702 391 89.07 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 251.472 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5109 Å2-0 Å20.7797 Å2
2---3.4472 Å20 Å2
3----8.2645 Å2
Refinement stepCycle: LAST / Resolution: 1.664→9.459 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms46 0 0 1 47
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00446
X-RAY DIFFRACTIONf_angle_d0.97562
X-RAY DIFFRACTIONf_dihedral_angle_d10.7415
X-RAY DIFFRACTIONf_chiral_restr0.0568
X-RAY DIFFRACTIONf_plane_restr0.0048
LS refinement shellResolution: 1.6644→9.4587 Å
RfactorNum. reflection% reflection
Rfree0.1983 18 -
Rwork0.1673 373 -
obs--89 %
Refinement TLS params.Method: refined / Origin x: 4.5323 Å / Origin y: 0.1096 Å / Origin z: 3.976 Å
111213212223313233
T-0.126 Å20.0821 Å2-0.0518 Å2--0.0788 Å20.0723 Å2---0.0487 Å2
L0.1003 °2-0.0319 °20.0506 °2-0.0184 °2-0.0233 °2--0.0647 °2
S0.0084 Å °-0.03 Å °-0.0565 Å °0.0231 Å °0.009 Å °0.0127 Å °-0.0046 Å °-0.0049 Å °-0.0009 Å °
Refinement TLS groupSelection details: all

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