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- PDB-3dg1: Segment SSTNVG derived from IAPP -

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Basic information

Entry
Database: PDB / ID: 3dg1
TitleSegment SSTNVG derived from IAPP
ComponentsSSTNVG from Islet Amyloid Polypeptide
KeywordsPROTEIN FIBRIL / steric zipper / IAPP / SSTNVG / Amyloid
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: 1.66 Å
AuthorsWiltzius, J.J. / Sievers, S.A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 2008
Title: Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin).
Authors: Wiltzius, J.J. / Sievers, S.A. / Sawaya, M.R. / Cascio, D. / Popov, D. / Riekel, C. / Eisenberg, D.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 3, 2015Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SSTNVG from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)5641
Polymers5641
Non-polymers00
Water362
1
A: SSTNVG from Islet Amyloid Polypeptide
x 6


Theoretical massNumber of molelcules
Total (without water)3,3816
Polymers3,3816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
crystal symmetry operation4_566-x+1/2,y+3/2,-z+11
crystal symmetry operation4_576-x+1/2,y+5/2,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)41.400, 4.785, 18.594
Angle α, β, γ (deg.)90.000, 115.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7-

HOH

DetailsThe biologic assembly is an amyloid-like fiber that can be generated by multiple application of the symmetry operators X, Y+n, Z and 1/2-X,n+(1/2)+Y,-Z+1, where n is an integer.

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Components

#1: Protein/peptide SSTNVG from Islet Amyloid Polypeptide


Mass: 563.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P10997*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 293 K / Method: vapor diffusion, hanging drop
Details: 30% MPD, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2007
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→90 Å / Num. all: 460 / Num. obs: 460 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.17 / Χ2: 1.472 / Net I/σ(I): 5.5
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.524 / Num. unique all: 37 / Χ2: 1.426 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine beta strand

Resolution: 1.66→18.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.826 / SU B: 2.359 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 45 9.8 %RANDOM
Rwork0.207 ---
obs0.211 459 95.62 %-
all-459 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.16 Å2 / Biso mean: 19.277 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.17 Å2
2---0.92 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.66→18.62 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms39 0 0 2 41
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02138
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.96751
X-RAY DIFFRACTIONr_angle_other_deg0.455351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.20855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg75.296301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.845155
X-RAY DIFFRACTIONr_chiral_restr0.0570.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0243
X-RAY DIFFRACTIONr_gen_planes_other00.025
X-RAY DIFFRACTIONr_nbd_refined0.0160.21
X-RAY DIFFRACTIONr_nbd_other0.2170.211
X-RAY DIFFRACTIONr_nbtor_refined0.1560.217
X-RAY DIFFRACTIONr_nbtor_other0.0820.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0760.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.27
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.23
X-RAY DIFFRACTIONr_mcbond_it1.634238
X-RAY DIFFRACTIONr_mcbond_other0.361212
X-RAY DIFFRACTIONr_mcangle_it2.248346
X-RAY DIFFRACTIONr_scbond_it1.45129
X-RAY DIFFRACTIONr_scangle_it1.45835
LS refinement shellResolution: 1.66→1.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.379 25 -
obs--69.44 %

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