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- PDB-4wbu: prion peptide -

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Basic information

Entry
Database: PDB / ID: 4wbu
Titleprion peptide
ComponentsPrP peptide
Keywordsde novo protein / membrane protein / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.15 Å
AuthorsYu, L. / Lee, S.-J. / Yee, V.
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structures of Polymorphic Prion Protein beta 1 Peptides Reveal Variable Steric Zipper Conformations.
Authors: Yu, L. / Lee, S.J. / Yee, V.C.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references / Derived calculations
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software
Item: _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PrP peptide
B: PrP peptide


Theoretical massNumber of molelcules
Total (without water)1,2532
Polymers1,2532
Non-polymers00
Water1629
1
A: PrP peptide
B: PrP peptide

A: PrP peptide
B: PrP peptide

A: PrP peptide
B: PrP peptide

A: PrP peptide
B: PrP peptide


Theoretical massNumber of molelcules
Total (without water)5,0148
Polymers5,0148
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)9.439, 17.792, 44.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT DISPLAYS ONLY A PORTION OF THE CRYSTAL LATTICE TO DEMONSTRATE THE CRYSTAL PACKING CONTENT. THE CRYSTAL PACKING IS FORMED BY A REPETITION IN BOTH DIRECTIONS OF THE PORTION INDICATED IN REMARK 350.

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Components

#1: Protein/peptide PrP peptide


Mass: 626.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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

CrystalDensity Matthews: 1.49 Å3/Da / Density % sol: 17.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 2.0 M ammonium sulfate, and 2.0 M NDSB-211

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 2627 / % possible obs: 87.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 3.56 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.001 / Net I/av σ(I): 11.957 / Net I/σ(I): 11.1 / Num. measured all: 14648
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.15-1.1930.1861971.09465.2
1.19-1.243.20.1712010.98175.8
1.24-1.33.90.1592401.1380.3
1.3-1.364.40.162381.06481
1.36-1.455.20.1482660.95295
1.45-1.565.70.122890.95996.3
1.56-1.726.40.1182750.93795.2
1.72-1.976.90.1072980.97196.1
1.97-2.487.50.0833070.97799
2.48-507.20.0813161.0790.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
SHELXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.15→22.28 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 16.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1665 116 4.45 %
Rwork0.15 2488 -
obs0.1507 2604 87.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 35.49 Å2 / Biso mean: 8.2041 Å2 / Biso min: 2.25 Å2
Refinement stepCycle: final / Resolution: 1.15→22.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms86 0 0 11 97
Biso mean---24.06 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892
X-RAY DIFFRACTIONf_angle_d1.382121
X-RAY DIFFRACTIONf_chiral_restr0.06811
X-RAY DIFFRACTIONf_plane_restr0.00415
X-RAY DIFFRACTIONf_dihedral_angle_d11.37535
LS refinement shellResolution: 1.1504→22.2847 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1665 116 -
Rwork0.15 2488 -
all-2604 -
obs--88 %

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