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- PDB-2onx: NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 ... -

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Entry
Database: PDB / ID: 2onx
TitleNNQQ peptide corresponding to residues 8-11 of yeast prion sup35 (alternate crystal form)
Componentspeptide corresponding to residues 8-11 of yeast prion sup35
KeywordsPROTEIN FIBRIL / steric zipper / beta sheets
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsSawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H. ...Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H. / Madsen, A.O. / Riekel, C. / 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 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: peptide corresponding to residues 8-11 of yeast prion sup35


Theoretical massNumber of molelcules
Total (without water)5021
Polymers5021
Non-polymers00
Water00
1
A: peptide corresponding to residues 8-11 of yeast prion sup35

A: peptide corresponding to residues 8-11 of yeast prion sup35

A: peptide corresponding to residues 8-11 of yeast prion sup35

A: peptide corresponding to residues 8-11 of yeast prion sup35


Theoretical massNumber of molelcules
Total (without water)2,0104
Polymers2,0104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)4.854, 16.014, 15.546
Angle α, β, γ (deg.)90.000, 96.910, 90.000
Int Tables number4
Space group name H-MP1211
DetailsOne sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the "a" unit cell dimension. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X,1/2+Y,1-Z, and repeated unit cell translations of this strand along the "a" unit cell dimension.

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Components

#1: Protein/peptide peptide corresponding to residues 8-11 of yeast prion sup35


Mass: 502.478 Da / Num. of mol.: 1 / Fragment: residues 8-11 / Source method: obtained synthetically

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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: 5.6
Details: 30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, ...Details: 30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. obs: 259 / % possible obs: 63.8 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.152 / Χ2: 1.15 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.621.20.299230.94926.1
1.62-1.781.10.277291.01142.6
1.78-2.041.30.322631.27979.7
2.04-2.561.40.173741.07285.1
2.56-901.90.101701.16983.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1yjp

1yjp


Resolution: 1.52→15.43 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.275 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 28 11.2 %RANDOM
Rwork0.172 ---
obs0.175 251 66.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.236 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20.39 Å2
2--0.16 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.52→15.43 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms35 0 0 0 35
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.85145
X-RAY DIFFRACTIONr_angle_other_deg0.926348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg49.819304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.152156
X-RAY DIFFRACTIONr_chiral_restr0.1480.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0241
X-RAY DIFFRACTIONr_gen_planes_other00.023
X-RAY DIFFRACTIONr_nbd_refined0.2010.21
X-RAY DIFFRACTIONr_nbd_other0.1650.216
X-RAY DIFFRACTIONr_nbtor_refined0.1580.212
X-RAY DIFFRACTIONr_nbtor_other0.0660.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.29
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.23
X-RAY DIFFRACTIONr_mcbond_it4.914226
X-RAY DIFFRACTIONr_mcbond_other1.2427
X-RAY DIFFRACTIONr_mcangle_it8.154331
X-RAY DIFFRACTIONr_scbond_it5.002216
X-RAY DIFFRACTIONr_scangle_it7.297314
LS refinement shellResolution: 1.52→1.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 2 -
Rwork0.556 9 -
obs-11 33.33 %

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