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- PDB-2onw: Structure of SSTSSA, a fibril forming peptide from Bovine Pancrea... -

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Basic information

Entry
Database: PDB / ID: 2onw
TitleStructure of SSTSSA, a fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A, residues 15-20)
Componentsfibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)
KeywordsPROTEIN FIBRIL / parallel face-to-face-Up/Up beta sheets / steric zipper
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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
X: fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)


Theoretical massNumber of molelcules
Total (without water)5231
Polymers5231
Non-polymers00
Water181
1
X: fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)

X: fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)

X: fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)

X: fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)


Theoretical massNumber of molelcules
Total (without water)2,0904
Polymers2,0904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation3_665-x+1,y+3/2,-z+1/21
Unit cell
Length a, b, c (Å)42.008, 4.830, 12.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a pair of sheets. Each sheet is comprised of beta strands generated by unit cell translations along the y-axis. The second sheet in the pair-of-sheet structures is generated by applying the operator -x+1, y+1/2, -z+1/2. In the second sheet also, beta strands are generated by unit cell translations along the y-axis.

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Components

#1: Protein/peptide fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)


Mass: 522.508 Da / Num. of mol.: 1 / Fragment: hinge loop region (residues 15-20) / Source method: obtained synthetically / Details: The peptide SSTSAA was commercially synthesized.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peptide concentration: 30 mg/ml, Reservoir: 0.1M HEPES-Na, pH 7.5, 10% v/v isopropanol, 20% PEG4000, 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: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.5→80 Å / Num. obs: 474 / % possible obs: 89.3 % / Biso Wilson estimate: 6.599 Å2 / Rmerge(I) obs: 0.174 / Χ2: 1.067 / Net I/σ(I): 3.9
Reflection shellResolution: 1.5→1.62 Å / Rmerge(I) obs: 0.434 / Num. unique all: 98 / Χ2: 1.084 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5 residue beta strand SSTSA with the C-terminal alanine absent

Resolution: 1.51→21 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.903 / SU B: 2.481 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 21 4.6 %RANDOM
Rwork0.157 ---
obs0.159 458 87.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.51→21 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms70 0 0 3 73
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02135
X-RAY DIFFRACTIONr_bond_other_d0.0010.0230
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.98347
X-RAY DIFFRACTIONr_angle_other_deg0.693370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.467154
X-RAY DIFFRACTIONr_chiral_restr0.0640.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0239
X-RAY DIFFRACTIONr_gen_planes_other00.025
X-RAY DIFFRACTIONr_nbd_other0.2070.211
X-RAY DIFFRACTIONr_nbtor_refined0.1220.216
X-RAY DIFFRACTIONr_nbtor_other0.0930.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0530.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.29
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.21
X-RAY DIFFRACTIONr_mcbond_it0.4881.536
X-RAY DIFFRACTIONr_mcbond_other0.1641.514
X-RAY DIFFRACTIONr_mcangle_it0.615246
X-RAY DIFFRACTIONr_scbond_it0.24335
X-RAY DIFFRACTIONr_scangle_it0.1374.51
X-RAY DIFFRACTIONr_rigid_bond_restr0.409371
X-RAY DIFFRACTIONr_sphericity_free0.34431
X-RAY DIFFRACTIONr_sphericity_bonded0.714366
LS refinement shellResolution: 1.51→1.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.723 1 -
Rwork0.249 25 -
obs-26 66.67 %

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