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- PDB-4w5p: Prp peptide -

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Basic information

Entry
Database: PDB / ID: 4w5p
TitlePrp peptide
ComponentsPrP peptide
Keywordsde novo protein / membrane protein / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.151 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 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 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

Downloads & links

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Assembly

Deposited unit
A: PrP peptide
B: PrP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4223
Polymers1,3032
Non-polymers1181
Water724
1
A: PrP peptide
B: PrP peptide
hetero molecules

A: PrP peptide
B: PrP peptide
hetero molecules

A: PrP peptide
B: PrP peptide
hetero molecules

A: PrP peptide
B: PrP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,68612
Polymers5,2148
Non-polymers4734
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Unit cell
Length a, b, c (Å)11.593, 17.152, 19.837
Angle α, β, γ (deg.)90.000, 100.700, 90.000
Int Tables number4
Space group name H-MP1211
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: 651.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.49 Å3/Da / Density % sol: 17.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris, 0.1 M ammonium acetate, and 40 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 2529 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.003 / Net I/av σ(I): 11.412 / Net I/σ(I): 7.4 / Num. measured all: 10485
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.15-1.191.40.1471350.9551.5
1.19-1.2420.1862181.01877.9
1.24-1.32.70.1992520.98888.4
1.3-1.363.10.1722421.04993.4
1.36-1.453.50.172871.01796.3
1.45-1.564.10.1742551.01498.1
1.56-1.724.80.1552851.00897.9
1.72-1.975.40.1522750.98699.3
1.97-2.486.20.1242840.99399.3
2.48-5060.12960.99899.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
SHELXphasing
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.151→19.492 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1508 108 4.29 %
Rwork0.1193 2408 -
obs0.1208 2516 90.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 23.35 Å2 / Biso mean: 9.4231 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: final / Resolution: 1.151→19.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms92 0 8 4 104
Biso mean--21.42 15.79 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009105
X-RAY DIFFRACTIONf_angle_d1.344142
X-RAY DIFFRACTIONf_chiral_restr0.04115
X-RAY DIFFRACTIONf_plane_restr0.00617
X-RAY DIFFRACTIONf_dihedral_angle_d13.90934
LS refinement shellResolution: 1.1508→19.4946 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1508 108 -
Rwork0.1193 2408 -
all-2516 -
obs--90 %

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