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- PDB-3dgj: NNFGAIL segment from Islet Amyloid Polypeptide (IAPP or amylin) -

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Basic information

Entry
Database: PDB / ID: 3dgj
TitleNNFGAIL segment from Islet Amyloid Polypeptide (IAPP or amylin)
ComponentsNNFGAIL peptide
KeywordsPROTEIN FIBRIL / IAPP / amylin / amyloid / steric zipper
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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: NNFGAIL peptide


Theoretical massNumber of molelcules
Total (without water)7481
Polymers7481
Non-polymers00
Water181
1
A: NNFGAIL peptide

A: NNFGAIL peptide

A: NNFGAIL peptide


Theoretical massNumber of molelcules
Total (without water)2,2443
Polymers2,2443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.190, 4.897, 31.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a fiber that can be generated by repeated application of unit cell translations along the b-cell dimension (X,Y+n,Z) where n is any integer.

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Components

#1: Protein/peptide NNFGAIL peptide


Mass: 747.840 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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 / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% ethylene glycol, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 9, 2007
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20.11 Å / Num. all: 481 / Num. obs: 481 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.747 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.98
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 901 / Num. unique obs: 62 / % possible all: 98.4

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Phasing

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

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.11 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.958 / SU B: 2.255 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 49 10.2 %RANDOM
Rwork0.16 ---
all0.166 481 --
obs0.166 481 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 12.59 Å2 / Biso mean: 5.491 Å2 / Biso min: 2.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.11 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms59 0 0 1 60
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02260
X-RAY DIFFRACTIONr_bond_other_d0.0010.0235
X-RAY DIFFRACTIONr_angle_refined_deg1.152.04182
X-RAY DIFFRACTIONr_angle_other_deg0.811388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.04826.6673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.588159
X-RAY DIFFRACTIONr_chiral_restr0.080.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0268
X-RAY DIFFRACTIONr_gen_planes_other00.0212
X-RAY DIFFRACTIONr_nbd_refined0.0280.23
X-RAY DIFFRACTIONr_nbd_other0.1790.228
X-RAY DIFFRACTIONr_nbtor_refined0.1530.230
X-RAY DIFFRACTIONr_nbtor_other0.0770.228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.25
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.040.25
X-RAY DIFFRACTIONr_mcbond_it1.26252
X-RAY DIFFRACTIONr_mcbond_other0.277215
X-RAY DIFFRACTIONr_mcangle_it1.484359
X-RAY DIFFRACTIONr_scbond_it0.802225
X-RAY DIFFRACTIONr_scangle_it1.133322
LS refinement shellResolution: 1.8→2.014 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.398 12 -
Rwork0.249 111 -
all-123 -
obs--98.4 %

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