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- PDB-4uby: Crystal structure of a polymorphic beta1 peptide -

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Basic information

Entry
Database: PDB / ID: 4uby
TitleCrystal structure of a polymorphic beta1 peptide
Componentsprion 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 13, 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 / database_2
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: prion peptide
B: prion peptide
C: prion peptide
D: prion peptide


Theoretical massNumber of molelcules
Total (without water)2,2594
Polymers2,2594
Non-polymers00
Water39622
1
A: prion peptide
B: prion peptide
C: prion peptide
D: prion peptide

A: prion peptide
B: prion peptide
C: prion peptide
D: prion peptide

A: prion peptide
B: prion peptide
C: prion peptide
D: prion peptide

A: prion peptide
B: prion peptide
C: prion peptide
D: prion peptide


Theoretical massNumber of molelcules
Total (without water)9,03416
Polymers9,03416
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_665x+1,y+1,z1
Unit cell
Length a, b, c (Å)11.666, 17.145, 19.073
Angle α, β, γ (deg.)79.760, 86.510, 90.200
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 in remark 350.

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Components

#1: Protein/peptide
prion peptide


Mass: 564.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.66 Å3/Da / Density % sol: 25.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, and 2 M ammonium sulfate

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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: 6346 / % possible obs: 80.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 2.67 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.016 / Net I/av σ(I): 16.26 / Net I/σ(I): 24.6 / Num. measured all: 18020
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1-1.041.90.1014551.26857.6
1.04-1.082.40.075210.93966.2
1.08-1.132.60.0665651.09974.1
1.13-1.192.80.0666220.95578.9
1.19-1.262.70.0756651.07484.2
1.26-1.362.70.0656461.00683.1
1.36-1.492.90.0646880.97787
1.49-1.713.20.0627350.95791.8
1.71-2.153.40.067441.02495.6
2.15-503.40.0587051.0389.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
SHELXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→13.822 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2.32 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1577 280 4.42 %Random selection
Rwork0.1201 6061 --
obs0.1218 6341 80.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.08 Å2 / Biso mean: 5.8555 Å2 / Biso min: 1.64 Å2
Refinement stepCycle: final / Resolution: 1→13.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms160 0 0 22 182
Biso mean---20.88 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006174
X-RAY DIFFRACTIONf_angle_d1.068231
X-RAY DIFFRACTIONf_chiral_restr0.05320
X-RAY DIFFRACTIONf_plane_restr0.00433
X-RAY DIFFRACTIONf_dihedral_angle_d9.81853
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 (%)
0.9996-1.25920.1321260.0992692281872
1.2592-13.82290.17081540.13073369352390

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