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- PDB-1uw3: The crystal structure of the globular domain of sheep prion protein -

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Basic information

Entry
Database: PDB / ID: 1uw3
TitleThe crystal structure of the globular domain of sheep prion protein
ComponentsPRION PROTEIN
KeywordsMEMBRANE PROTEIN / TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHY / CREUTZFELD JACOB DISEASE
Function / homology
Function and homology information


side of membrane / tubulin binding / protein homooligomerization / microtubule binding / copper ion binding / Golgi apparatus / identical protein binding / plasma membrane
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily ...Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / PHOSPHATE ION / Major prion protein
Similarity search - Component
Biological speciesOVIS ARIES (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHaire, L.F. / Whyte, S.M. / Vasisht, N. / Gill, A.C. / Verma, C. / Dodson, E.J. / Dodson, G.G. / Bayley, P.M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of the Globular Domain of Sheep Prion Protein
Authors: Haire, L.F. / Whyte, S.M. / Vasisht, N. / Gill, A.C. / Verma, C. / Dodson, E.J. / Dodson, G.G. / Bayley, P.M.
History
DepositionJan 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0113
Polymers12,6091
Non-polymers4022
Water1,27971
1
A: PRION PROTEIN
hetero molecules

A: PRION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0236
Polymers25,2182
Non-polymers8054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1840 Å2
ΔGint-5 kcal/mol
Surface area14640 Å2
MethodPQS
Unit cell
Length a, b, c (Å)85.068, 29.045, 45.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

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Components

#1: Protein PRION PROTEIN / SHEEP PRION PROTEIN


Mass: 12609.001 Da / Num. of mol.: 1 / Fragment: RESIDUES 128-233 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / References: UniProt: P23907
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growpH: 8.6 / Details: pH 8.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.6 / PH range high: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
20.8-1.3 Msodium potassium phosphate1reservoirpH7.4-8.6

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Data collection

DiffractionMean temperature: 165 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.414
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.414 Å / Relative weight: 1
ReflectionResolution: 2.05→19.3 Å / Num. obs: 7095 / % possible obs: 93.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 2.05→2.13 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 78
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 83.7 % / Rmerge(I) obs: 0.465

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMAC5.1.9999refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I4M

1i4m


Resolution: 2.05→84.51 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.829 / SU B: 5.928 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES 125 - 137 ARE POORLY ORDERED, AND PROBABLY TAKE UP MORE THAN ONE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.33 326 4.6 %RANDOM
Rwork0.222 ---
obs0.227 6769 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.05→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 21 71 975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9331255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4145105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62723.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.59215154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.17158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02741
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2474
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2840.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2781.5542
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9462858
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4893442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5854.5397
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.378 19
Rwork0.26 420
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.319 / Rfactor Rwork: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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