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- PDB-4w5l: Crystal structure of a prp peptide -

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Basic information

Entry
Database: PDB / ID: 4w5l
TitleCrystal structure of a prp peptide
ComponentsPrP peptide
Keywordsde novo protein / membrane protein / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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


Theoretical massNumber of molelcules
Total (without water)1,3312
Polymers1,3312
Non-polymers00
Water19811
1
A: PrP peptide
B: PrP peptide
x 6


Theoretical massNumber of molelcules
Total (without water)7,98912
Polymers7,98912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_566x,y+1,z+11
crystal symmetry operation3_555-x+1/2,y+1/2,-z1
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
Unit cell
Length a, b, c (Å)50.483, 21.113, 9.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-204-

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: 665.738 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.: 11 / 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: 1.89 Å3/Da / Density % sol: 34.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M tri-sodium citrate, 0.1 M Hepes pH 7.5, and 30 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7749 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 4814 / % possible obs: 80.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 5.63 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.002 / Net I/av σ(I): 16.97 / Net I/σ(I): 14.6 / Num. measured all: 15931
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1-1.041.80.1442530.99143.2
1.04-1.082.40.113420.94559.2
1.08-1.1330.0863881.03867.5
1.13-1.1930.0764681.01377.5
1.19-1.262.80.0894661.01882.5
1.26-1.363.10.0795380.9788.1
1.36-1.493.40.085521.00296.2
1.49-1.713.70.0645791.01897.1
1.71-2.154.20.0456001.01496.3
2.15-504.20.0456280.98391.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
SHELXphasing
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1→13.159 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 213 4.51 %
Rwork0.1682 4507 -
obs0.1686 4720 79.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.42 Å2 / Biso mean: 10.077 Å2 / Biso min: 3.08 Å2
Refinement stepCycle: final / Resolution: 1→13.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94 0 0 11 105
Biso mean---35.85 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005108
X-RAY DIFFRACTIONf_angle_d1.208144
X-RAY DIFFRACTIONf_chiral_restr0.04514
X-RAY DIFFRACTIONf_plane_restr0.00419
X-RAY DIFFRACTIONf_dihedral_angle_d8.69136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.999-1.25850.1638890.1431783187265
1.2585-13.16040.18081240.17612724284893

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