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- PDB-2ol9: Peptide corresponding to residues 170-175 of human prion -

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Basic information

Entry
Database: PDB / ID: 2ol9
TitlePeptide corresponding to residues 170-175 of human prion
Componentspeptide from human prion
KeywordsPROTEIN FIBRIL / steric zipper / beta sheet
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsApostol, M.A. / 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 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 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Dec 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 1.6Apr 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 human prion


Theoretical massNumber of molelcules
Total (without water)7231
Polymers7231
Non-polymers00
Water905
1
A: peptide from human prion

A: peptide from human prion


Theoretical massNumber of molelcules
Total (without water)1,4452
Polymers1,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)14.002, 4.879, 15.100
Angle α, β, γ (deg.)75.230, 75.880, 78.890
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide peptide from human prion


Mass: 722.704 Da / Num. of mol.: 1 / Fragment: residues 170-175 / Source method: obtained synthetically
Details: This sequence is taken from residues 170-175 of human prion
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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
Details: 200 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.8856
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 48.7 / Number: 9598 / Rmerge(I) obs: 0.036 / Χ2: 1.2 / D res high: 0.85 Å / D res low: 90 Å / Num. obs: 2681 / % possible obs: 82.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
1.83909610.0271.073.8
1.451.8393.110.0341.1863.7
1.271.4510010.0371.153.8
1.151.2785.510.041.1663.8
1.071.1590.210.0361.1433.7
1.011.0799.710.0481.3873.8
0.961.0192.410.0551.1963.6
0.920.9679.510.0671.3013.3
0.880.9251.910.0781.22.7
0.850.8833.510.0781.1392.3
ReflectionResolution: 0.85→90 Å / Num. all: 2681 / Num. obs: 2681 / % possible obs: 82.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 4.4 Å2 / Rmerge(I) obs: 0.036 / Χ2: 1.195 / Net I/σ(I): 48.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
0.85-0.882.30.0781071.13933.5
0.88-0.922.70.0781751.251.9
0.92-0.963.30.0672671.30179.5
0.96-1.013.60.0553041.19692.4
1.01-1.073.80.0483091.38799.7
1.07-1.153.70.0362931.14390.2
1.15-1.273.80.042821.16685.5
1.27-1.453.80.0373221.15100
1.45-1.833.70.0343091.18693.1
1.83-903.80.0273131.0796

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealized 6 residue beta strand

Resolution: 0.85→14.29 Å / Cor.coef. Fo:Fc: 0.992 / Cor.coef. Fo:Fc free: 0.989 / SU B: 0.242 / SU ML: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.078 134 5 %RANDOM
Rwork0.073 ---
all0.073 2680 --
obs0.073 2680 82.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 1.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.03 Å2-0.06 Å2
2---0.04 Å20.06 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 0.85→14.29 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms51 0 0 5 56
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02151
X-RAY DIFFRACTIONr_bond_other_d0.0010.0230
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.82868
X-RAY DIFFRACTIONr_angle_other_deg0.505373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg52.08285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.571157
X-RAY DIFFRACTIONr_chiral_restr0.0730.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0262
X-RAY DIFFRACTIONr_gen_planes_other00.0210
X-RAY DIFFRACTIONr_nbd_refined0.0810.24
X-RAY DIFFRACTIONr_nbd_other0.190.216
X-RAY DIFFRACTIONr_nbtor_refined0.1760.220
X-RAY DIFFRACTIONr_nbtor_other0.0720.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0340.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.21
X-RAY DIFFRACTIONr_mcbond_it0.3941.539
X-RAY DIFFRACTIONr_mcbond_other0.0731.511
X-RAY DIFFRACTIONr_mcangle_it0.484247
X-RAY DIFFRACTIONr_scbond_it0.651324
X-RAY DIFFRACTIONr_scangle_it0.8574.521
X-RAY DIFFRACTIONr_rigid_bond_restr0.6883107
X-RAY DIFFRACTIONr_sphericity_free1.68635
X-RAY DIFFRACTIONr_sphericity_bonded0.569381
LS refinement shellResolution: 0.85→0.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.052 4 -
Rwork0.175 72 -
obs-76 31.4 %

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