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- PDB-3fpo: HSSNNF segment from Islet Amyloid Polypeptide (IAPP or Amylin) -

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Basic information

Entry
Database: PDB / ID: 3fpo
TitleHSSNNF segment from Islet Amyloid Polypeptide (IAPP or Amylin)
ComponentsHSSNNF hexapeptide segment from Islet Amyloid Polypeptide
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly ...: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / positive regulation of cAMP-mediated signaling / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
Islet amyloid polypeptide
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsWiltzius, J.J.W. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular mechanisms for protein-encoded inheritance.
Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: HSSNNF hexapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)7061
Polymers7061
Non-polymers00
Water724
1
A: HSSNNF hexapeptide segment from Islet Amyloid Polypeptide

A: HSSNNF hexapeptide segment from Islet Amyloid Polypeptide

A: HSSNNF hexapeptide segment from Islet Amyloid Polypeptide

A: HSSNNF hexapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)2,8234
Polymers2,8234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_355x-2,y,z1
Unit cell
Length a, b, c (Å)4.822, 16.391, 23.476
Angle α, β, γ (deg.)90.000, 92.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide HSSNNF hexapeptide segment from Islet Amyloid Polypeptide


Mass: 705.697 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HSSNNF (residues 18-23) from human Islet Amyloid Polypeptide, synthesized
References: UniProt: P10997*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. all: 568 / Num. obs: 568 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.159 / Χ2: 1.471 / Net I/σ(I): 9.505
Reflection shellResolution: 1.5→1.62 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2 / Num. unique all: 99 / Χ2: 2.435 / % possible all: 75.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.893 / SU B: 1.327 / SU ML: 0.046 / SU R Cruickshank DPI: 0.095 / SU Rfree: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.154 53 9.4 %RANDOM
Rwork0.139 ---
obs0.14 562 92.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 29.38 Å2 / Biso mean: 5.454 Å2 / Biso min: 2.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.06 Å2
2--0.88 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.45 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms50 0 0 4 54
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0230
X-RAY DIFFRACTIONr_angle_refined_deg0.7031.79668
X-RAY DIFFRACTIONr_angle_other_deg0.535372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.15355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg57.475254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.176156
X-RAY DIFFRACTIONr_chiral_restr0.0760.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0260
X-RAY DIFFRACTIONr_gen_planes_other00.0212
X-RAY DIFFRACTIONr_nbd_refined0.1460.23
X-RAY DIFFRACTIONr_nbd_other0.20.213
X-RAY DIFFRACTIONr_nbtor_refined0.1710.221
X-RAY DIFFRACTIONr_nbtor_other0.070.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.24
X-RAY DIFFRACTIONr_mcbond_it0.888235
X-RAY DIFFRACTIONr_mcbond_other0.142211
X-RAY DIFFRACTIONr_mcangle_it1.596347
X-RAY DIFFRACTIONr_scbond_it1.065226
X-RAY DIFFRACTIONr_scangle_it1.049321
LS refinement shellResolution: 1.5→1.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.212 13 -
Rwork0.204 126 -
all-139 -
obs--77.22 %

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