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- PDB-4w71: Crystal structure of a prion peptide -

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Basic information

Entry
Database: PDB / ID: 4w71
TitleCrystal structure of a prion peptide
ComponentsPrP peptide
Keywordsde novo protein / membrane protein / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 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
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Derived calculations
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._citation.journal_id_CSD / _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 1.4Dec 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

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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)1,3602
Polymers1,3602
Non-polymers00
Water18010
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)5,4388
Polymers5,4388
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)9.467, 10.382, 22.343
Angle α, β, γ (deg.)81.800, 81.400, 67.950
Int Tables number1
Space group name H-MP1
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

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Components

#1: Protein/peptide PrP peptide


Mass: 679.764 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.: 10 / 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

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 16.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris and 10-14 % ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 3028 / % possible obs: 72.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 2.34 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.055 / Net I/av σ(I): 12.316 / Net I/σ(I): 20.4 / Num. measured all: 7387
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1-1.041.60.1461841.54843
1.04-1.081.80.1072271.05455.4
1.08-1.132.20.0962881.00267.1
1.13-1.192.30.0972850.9667.4
1.19-1.262.20.1062811.07368.9
1.26-1.362.30.0853190.97573.8
1.36-1.492.50.093331.06780
1.49-1.712.60.083451.04685
1.71-2.152.90.0663871.08790.4
2.15-503.10.063791.0590.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SHELXphasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→10.997 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 2.25 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1534 124 4.11 %
Rwork0.1176 2894 -
obs0.119 3018 71.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 28.33 Å2 / Biso mean: 5.7137 Å2 / Biso min: 1.2 Å2
Refinement stepCycle: final / Resolution: 1→10.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94 0 0 10 104
Biso mean---19.98 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009113
X-RAY DIFFRACTIONf_angle_d1.327152
X-RAY DIFFRACTIONf_chiral_restr0.05118
X-RAY DIFFRACTIONf_plane_restr0.00518
X-RAY DIFFRACTIONf_dihedral_angle_d11.69634
LS refinement shellResolution: 0.9996→10.9972 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1534 124 -
Rwork0.1176 2894 -
all-3018 -
obs--72 %

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