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- PDB-3fva: NNQNTF segment from elk prion -

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Basic information

Entry
Database: PDB / ID: 3fva
TitleNNQNTF segment from elk prion
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril / Cell membrane / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane / Prion
Function / homology
Function and homology information


side of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / plasma membrane
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / 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
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.458 Å
AuthorsApostol, M.I. / Eisenberg, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular mechanisms for protein-encoded inheritance.
Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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: Major prion protein


Theoretical massNumber of molelcules
Total (without water)7371
Polymers7371
Non-polymers00
Water362
1
A: Major prion protein
x 6


Theoretical massNumber of molelcules
Total (without water)4,4206
Polymers4,4206
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
crystal symmetry operation2_464-x-1,y+3/2,-z-11
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Unit cell
Length a, b, c (Å)18.061, 4.840, 21.362
Angle α, β, γ (deg.)90.000, 100.100, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological unit is an indefinitely long pair of sheets (a protofibril). One sheet is constructed from chain A (X,Y,Z) and unit cell translations along b cell dimension (e.g. X,Y+1,Z; X,Y-1,Z). The second sheet is constructed from crystallographic symmetry operator -x-1,y+1/2,-z-1 and unit cell translations along the b dimension (e.g. -x-1,y+3/2,-z-1). There is an additional polymorph of the biological unit (also a pair of beta sheets). One sheet is constructed from chain A (X,Y,Z) and unit cell translations along b cell dimension (e.g. X,Y+1,Z; X,Y-1,Z). The second sheet is constructed from crystallographic symmetry operator -x,y+1/2,-z-1 and unit cell translations along the b dimension (e.g. -x,y+3/2,-z-1).

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Components

#1: Protein/peptide Major prion protein / PrP


Mass: 736.730 Da / Num. of mol.: 1 / Fragment: NNQNTF (residues 173-178) / Source method: obtained synthetically / Details: NNQNTF (residues 173-178) from elk prion protein / References: UniProt: P67986
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.248 Å3/Da / Density % sol: 1.417 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Ammonium Sulfate, 0.1M Tris pH 8.5, 25% PEG 3350, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.946496 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946496 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 750 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.137 / Χ2: 1.031 / Net I/σ(I): 7.197
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.54.30.273791.082100
1.5-1.564.80.216721.03298.6
1.56-1.635.40.205671.02489.3
1.63-1.726.10.183581.019100
1.72-1.8360.227751.048100
1.83-1.976.10.137711.051100
1.97-2.176.10.135781.023100
2.17-2.485.50.164831.02798.8
2.48-3.125.50.09711.012100
3.12-304.90.081961.006100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.458→21.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.914 / SU B: 0.981 / SU ML: 0.038 / SU R Cruickshank DPI: 0.08 / SU Rfree: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 40 5.4 %RANDOM
Rwork0.162 ---
obs0.163 747 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 11.11 Å2 / Biso mean: 0.702 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.32 Å2
2--0.17 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.458→21.03 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms52 0 0 2 54
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02152
X-RAY DIFFRACTIONr_angle_refined_deg0.771.82670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.676285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.549157
X-RAY DIFFRACTIONr_chiral_restr0.0740.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0247
X-RAY DIFFRACTIONr_nbd_refined0.150.28
X-RAY DIFFRACTIONr_nbtor_refined0.2880.234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.216
X-RAY DIFFRACTIONr_mcbond_it0.4091.531
X-RAY DIFFRACTIONr_mcangle_it0.654248
X-RAY DIFFRACTIONr_scbond_it0.729323
X-RAY DIFFRACTIONr_scangle_it0.9464.522
LS refinement shellResolution: 1.458→1.496 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 2 -
Rwork0.236 40 -
all-42 -
obs--85.71 %

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