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- PDB-3ftr: Structure of an amyloid forming peptide SSTNVG from IAPP (alterna... -

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Basic information

Entry
Database: PDB / ID: 3ftr
TitleStructure of an amyloid forming peptide SSTNVG from IAPP (alternate polymorph)
ComponentsSSTNVG 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: 1.61 Å
AuthorsLandau, M. / 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 13, 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: SSTNVG FROM ISLET AMYLOID POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)5641
Polymers5641
Non-polymers00
Water543
1
A: SSTNVG FROM ISLET AMYLOID POLYPEPTIDE

A: SSTNVG FROM ISLET AMYLOID POLYPEPTIDE

A: SSTNVG FROM ISLET AMYLOID POLYPEPTIDE

A: SSTNVG FROM ISLET AMYLOID POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)2,2544
Polymers2,2544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)16.590, 4.789, 40.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 3 / 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: 7.5
Details: reservoir contained 20% w/v PEG-3000, 0.1M HEPES, 0.2M NaCl, pH 7.5, 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 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. obs: 503 / % possible obs: 92.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.149 / Χ2: 1.006 / Net I/σ(I): 6.462
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.722.80.499780.76285.7
1.72-1.92.90.422860.96387.8
1.9-2.174.60.2391011.10693.5
2.17-2.745.70.2211081.03594.7
2.74-905.40.091300.98998.5

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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
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→20.11 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.864 / SU B: 1.99 / SU ML: 0.069 / SU R Cruickshank DPI: 0.15 / SU Rfree: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 48 9.9 %RANDOM
Rwork0.223 ---
obs0.226 486 92.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 32.99 Å2 / Biso mean: 9.598 Å2 / Biso min: 3.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2---1.31 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.61→20.11 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms39 0 0 3 42
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02138
X-RAY DIFFRACTIONr_bond_other_d0.0070.0220
X-RAY DIFFRACTIONr_angle_refined_deg0.9131.96751
X-RAY DIFFRACTIONr_angle_other_deg0.593351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.12155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.332301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.329155
X-RAY DIFFRACTIONr_chiral_restr0.0810.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0243
X-RAY DIFFRACTIONr_gen_planes_other00.025
X-RAY DIFFRACTIONr_mcbond_it1.74229
X-RAY DIFFRACTIONr_mcbond_other0.407212
X-RAY DIFFRACTIONr_mcangle_it2.574346
X-RAY DIFFRACTIONr_scbond_it1.27229
X-RAY DIFFRACTIONr_scangle_it1.78635
LS refinement shellResolution: 1.61→1.797 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.396 11 -
Rwork0.265 101 -
all-112 -
obs--88.19 %

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