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- PDB-4w5m: Prp peptide -

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Basic information

Entry
Database: PDB / ID: 4w5m
TitlePrp peptide
ComponentsPrP peptide
Keywordsde novo protein / membrane protein / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 1.1Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,4863
Polymers1,3682
Non-polymers1181
Water724
1
A: PrP peptide
B: PrP peptide
hetero molecules
x 5


  • defined by author
  • 7.43 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)7,42915
Polymers6,83810
Non-polymers5915
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Unit cell
Length a, b, c (Å)47.481, 9.437, 22.621
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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: 683.776 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: 1.85 Å3/Da / Density % sol: 33.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris, 2% 2-methyl-2,4-pentanediol (MPD), and 1.1 M ammonium sulfate

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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 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 2911 / % possible obs: 86.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.071 / Χ2: 1.026 / Net I/av σ(I): 12.776 / Net I/σ(I): 11.1 / Num. measured all: 7028
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.2-1.241.50.0991540.95249.2
1.24-1.291.80.0972451.05972.3
1.29-1.3520.1022651.03977.9
1.35-1.422.30.1012911.03192.1
1.42-1.512.40.0923281.12496.2
1.51-1.632.60.0863201.00198.2
1.63-1.792.80.0793111.01298.1
1.79-2.052.80.0733430.95199.1
2.05-2.592.80.0653371.05398.8
2.59-502.50.0653171.0385.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
SHELXphasing
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→23.644 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 119 4.13 %
Rwork0.1934 --
obs0.1955 2884 86.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.55 Å2 / Biso mean: 17.1338 Å2 / Biso min: 6.02 Å2
Refinement stepCycle: final / Resolution: 1.2→23.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94 0 8 4 106
Biso mean--34.37 34.24 -
Num. residues----14

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