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- PDB-2olx: Structure of NNQQ Peptide from Yeast Prion SUP35 -

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Basic information

Entry
Database: PDB / ID: 2olx
TitleStructure of NNQQ Peptide from Yeast Prion SUP35
ComponentsNNQQ peptide derived from Yeast Prion Sup35
KeywordsPROTEIN FIBRIL / steric zipper / glutamine zipper / polar zipper / asparagine zipper
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsNelson, R. / 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 19, 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: NNQQ peptide derived from Yeast Prion Sup35


Theoretical massNumber of molelcules
Total (without water)5021
Polymers5021
Non-polymers00
Water00
1
A: NNQQ peptide derived from Yeast Prion Sup35

A: NNQQ peptide derived from Yeast Prion Sup35

A: NNQQ peptide derived from Yeast Prion Sup35


  • defined by author
  • 1.51 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)1,5073
Polymers1,5073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)15.479, 4.915, 30.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsOne sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X,1/2+Y,1/2-Z, and repeated unit cell translations of this strand along the b axis.

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Components

#1: Protein/peptide NNQQ peptide derived from 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 / Details: 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: Dec 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.4→90 Å / Num. all: 426 / Num. obs: 426 / % possible obs: 74.9 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.124 / Χ2: 1.072 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.452.80.209250.954.3
1.45-1.512.60.199341.09559.6
1.51-1.582.60.144271.1446.6
1.58-1.662.70.139271.07844.3
1.66-1.762.60.121311.14666
1.76-1.93.20.139460.99995.8
1.9-2.093.10.153511.10294.4
2.09-2.393.30.148600.98990.9
2.39-3.023.90.124521.02891.2
3.02-9030.097731.21297.3

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Processing

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

Resolution: 1.42→15.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.75 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 39 9.4 %RANDOM
Rwork0.183 ---
obs0.188 413 74.28 %-
all-426 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.984 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 1.42→15.28 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms35 0 0 0 35
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.85145
X-RAY DIFFRACTIONr_angle_other_deg0.615348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.13553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.192304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.806156
X-RAY DIFFRACTIONr_chiral_restr0.1660.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0241
X-RAY DIFFRACTIONr_gen_planes_other00.023
X-RAY DIFFRACTIONr_nbd_other0.180.213
X-RAY DIFFRACTIONr_nbtor_refined0.1330.213
X-RAY DIFFRACTIONr_nbtor_other0.0790.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.21
X-RAY DIFFRACTIONr_mcbond_it6.472228
X-RAY DIFFRACTIONr_mcbond_other3.01327
X-RAY DIFFRACTIONr_mcangle_it6.638331
X-RAY DIFFRACTIONr_scbond_it9.714214
X-RAY DIFFRACTIONr_scangle_it7.745314
X-RAY DIFFRACTIONr_rigid_bond_restr6.143361
X-RAY DIFFRACTIONr_sphericity_bonded6.513354
LS refinement shellResolution: 1.42→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 3 -
Rwork0.237 14 -
obs-17 45.95 %

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