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- PDB-4tut: Structure of a Prion peptide -

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Basic information

Entry
Database: PDB / ID: 4tut
TitleStructure of a Prion peptide
ComponentsPrion peptide: GLY-GLY-TYR-MET-LEU-GLY
KeywordsMEMBRANE PROTEIN / DE NOVO PROTEIN / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.9 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
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Structure summary
Revision 1.2Nov 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_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prion peptide: GLY-GLY-TYR-MET-LEU-GLY


Theoretical massNumber of molelcules
Total (without water)5971
Polymers5971
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)10.395, 9.731, 17.382
Angle α, β, γ (deg.)90.000, 105.940, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein/peptide Prion peptide: GLY-GLY-TYR-MET-LEU-GLY


Mass: 596.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.42 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 1.3 M sodium acetate, and 25 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.72932 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. obs: 1862 / % possible obs: 71.4 % / Redundancy: 4 % / Biso Wilson estimate: 1.55 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.019 / Net I/av σ(I): 20.908 / Net I/σ(I): 27.4 / Num. measured all: 7403
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
0.9-0.931.90.068821.04732.3
0.93-0.972.40.071301.05548.3
0.97-1.012.80.0681351.03556.5
1.01-1.073.10.071651.02864.5
1.07-1.133.60.062021.02777.7
1.13-1.223.90.0592091.01980.4
1.22-1.344.20.0682121.02180.3
1.34-1.544.50.0682301.04187.1
1.54-1.944.90.0672370.96890.5
1.94-505.40.0672601.02792.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→9.996 Å / SU ML: 0.03 / Cross valid method: FREE R-VALUE / σ(F): 2.32 / Phase error: 6.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.098 80 4.3 %Random selection
Rwork0.07 1780 --
obs0.0712 1860 71.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 12.32 Å2 / Biso mean: 2.497 Å2 / Biso min: 1.31 Å2
Refinement stepCycle: final / Resolution: 0.9→9.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41 0 0 5 46
Biso mean---7.7 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741
X-RAY DIFFRACTIONf_angle_d1.36553
X-RAY DIFFRACTIONf_chiral_restr0.0584
X-RAY DIFFRACTIONf_plane_restr0.017
X-RAY DIFFRACTIONf_dihedral_angle_d6.07414
LS refinement shellHighest resolution: 0.8996 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.098 80 -
Rwork0.07 1780 -
all-1860 -
obs--71 %

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