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- PDB-2okz: MVGGVV peptide derived from Alzheimer's A-beta -

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Basic information

Entry
Database: PDB / ID: 2okz
TitleMVGGVV peptide derived from Alzheimer's A-beta
Componentspeptide from Alzheimer's A-beta
KeywordsPROTEIN FIBRIL / steric zipper
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSawaya, M.R. / Sambashivan, S. / 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 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 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: peptide from Alzheimer's A-beta
B: peptide from Alzheimer's A-beta


Theoretical massNumber of molelcules
Total (without water)1,1212
Polymers1,1212
Non-polymers00
Water00
1
A: peptide from Alzheimer's A-beta

B: peptide from Alzheimer's A-beta

A: peptide from Alzheimer's A-beta
B: peptide from Alzheimer's A-beta


Theoretical massNumber of molelcules
Total (without water)2,2434
Polymers2,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_556-x,y+1/2,-z+11
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)15.148, 9.576, 23.732
Angle α, β, γ (deg.)90.000, 96.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide peptide from Alzheimer's A-beta


Mass: 560.707 Da / Num. of mol.: 2 / Fragment: residues 35-40 / Source method: obtained synthetically
Details: This sequence corresponds to residues 35-40 of human A-beta peptide

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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: 4.6
Details: 0.2 M CaCl2, 20% isopropanol, 0.1 M Na acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jul 16, 2005
RadiationMonochromator: channel-cut Si-111 monochromator and an ellipsoidal mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 650 / Num. obs: 650 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.158 / Χ2: 1.073 / Net I/σ(I): 4.2
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.447 / Num. unique all: 123 / Χ2: 1.082 / % possible all: 89.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MVGGVV from space group P1

Resolution: 1.8→23.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.396 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 35 5.4 %RANDOM
Rwork0.213 ---
obs0.217 648 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.24 Å2
2---1.77 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.56 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms76 0 0 0 76
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0240
X-RAY DIFFRACTIONr_angle_refined_deg1.6852.05798
X-RAY DIFFRACTIONr_angle_other_deg0.6333102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.554510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5031512
X-RAY DIFFRACTIONr_chiral_restr0.0870.214
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0278
X-RAY DIFFRACTIONr_gen_planes_other00.0210
X-RAY DIFFRACTIONr_nbd_refined0.1460.26
X-RAY DIFFRACTIONr_nbd_other0.2040.226
X-RAY DIFFRACTIONr_nbtor_refined0.1420.234
X-RAY DIFFRACTIONr_nbtor_other0.0950.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.21
X-RAY DIFFRACTIONr_mcbond_it6.037267
X-RAY DIFFRACTIONr_mcbond_other2.15226
X-RAY DIFFRACTIONr_mcangle_it5.903388
X-RAY DIFFRACTIONr_scbond_it5.729218
X-RAY DIFFRACTIONr_scangle_it7.162310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.138 1 -
Rwork0.163 24 -
obs-25 52.08 %

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