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- PDB-2onv: Crystal Structure of the amyloid-fibril forming peptide GGVVIA de... -

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Entry
Database: PDB / ID: 2onv
TitleCrystal Structure of the amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta (Abeta37-42).
Componentsamyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta
KeywordsPROTEIN FIBRIL / steric zipper / beta sheets
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSambashivan, S. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A.O. / Riekel, C. / Eisenberg, D.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: 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: amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta


Theoretical massNumber of molelcules
Total (without water)5151
Polymers5151
Non-polymers00
Water543
1
A: amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta

A: amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta

A: amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta

A: amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta


Theoretical massNumber of molelcules
Total (without water)2,0584
Polymers2,0584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)16.760, 41.134, 4.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a pair of sheets. Beta strands within the sheet are generated by unit cell translations along the z-axis. The second sheet in the pair of sheets is generated by applying the symmetry operator x+1/2, -y+1/2, -z. Within the second sheet also, beta strands are generated by unit cell translations along the z-axis.

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Components

#1: Protein/peptide amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta


Mass: 514.616 Da / Num. of mol.: 1 / Fragment: residues 37-42 / Source method: obtained synthetically / Details: Peptide was commercially synthesized by CSBio.
#2: Water ChemComp-HOH / 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

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 23.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Peptide concentration: 15.0 mg/ml, Peptide:reservoir:additive ratio 5:4:1, Reservoir: 2.0M Ammonium sulfate, Additive: 3.0% 0.1M hexamine cobalt (III) chloride , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. obs: 532 / % possible obs: 96.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.962 Å2 / Rmerge(I) obs: 0.192 / Χ2: 1.085 / Net I/σ(I): 12.6
Reflection shellResolution: 1.6→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.42 / Num. unique all: 87 / Χ2: 1.102 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Extended beta strand GGVVIA

Resolution: 1.61→20.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.852 / SU B: 4.479 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.299 51 9.9 %RANDOM
Rwork0.228 ---
obs0.235 515 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.61→20.57 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms36 0 0 3 39
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02335
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218
X-RAY DIFFRACTIONr_angle_refined_deg1.8592.0447
X-RAY DIFFRACTIONr_angle_other_deg1.041346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.738154
X-RAY DIFFRACTIONr_chiral_restr0.0840.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0239
X-RAY DIFFRACTIONr_gen_planes_other00.025
X-RAY DIFFRACTIONr_nbd_refined0.0260.21
X-RAY DIFFRACTIONr_nbd_other0.1820.212
X-RAY DIFFRACTIONr_nbtor_refined0.1580.217
X-RAY DIFFRACTIONr_nbtor_other0.0780.219
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3520.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.23
X-RAY DIFFRACTIONr_mcbond_it1.3881.535
X-RAY DIFFRACTIONr_mcbond_other0.1371.513
X-RAY DIFFRACTIONr_mcangle_it1.773243
X-RAY DIFFRACTIONr_scbond_it0.65137
X-RAY DIFFRACTIONr_scangle_it0.894.54
LS refinement shellResolution: 1.61→1.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.007 1 -
Rwork0.324 22 -
obs-23 88.46 %

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