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PDB | 3NVF | IIHFGS segment 138-143 from human prion

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Internal ID
72514
PDB Entry ID
3NVF
Title
IIHFGS segment 138-143 from human prion
Authors
Apostol, M.I.,Sawaya, M.R.,Eisenberg, D.
Primary Citation
AuthorsApostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., Eisenberg, D.
TitleAtomic structures suggest determinants of transmission barriers in Mammalian prion disease.
JournalBiochemistry, v.50, pp.2456 - 2463, 2011
AbstractView
Pubmed21323366
DOI10.1021/bi101803k
 
History
Deposition: 2010-07-08Release: 2011-03-02Last Modified: 2011-04-13
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.800.2130.2120.226P 21 21 2
Unit Cell
Length [Å]a27.55b31.02c4.80
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Major prion proteinA
Functional Class
Related PDB Entries
IDDetails
3NVEMMHFGN hexapeptide (residues 138-143) from golden hamster prion protein
3NVGMIHFGN hexapeptide (residues 137-142) from mouse prion protein
3NVHMIHFGND (residues 137-143) from mouse prion protein
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
MPD(4S)-2-METHYL-2,4-PENTANEDIOLC6H14O2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordPROTEIN FIBRIL
Textamyloid-like protofibril, PROTEIN FIBRIL
 
Polymeric Molecules
Chain A
DescriptionMajor prion protein
Polymer typepolypeptide
Formula Weight673.8
Source Methodsynthetic
Entity NamePrP, PrP27-30, PrP33-35C, ASCR
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
MPD(4S)-2-METHYL-2,4-PENTANEDIOLC6H14O2118.175View
Crystallization Experiments
Methodvapor diffusion, hanging drop
PH7.4
Temperature298.0
Details100mM Tris pH 7.4, 25% MPD, vapor diffusion, hanging drop, temperature 298K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
27.5531.024.80
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 2
Diffraction Detector
DetectorCCD
TypeMAR CCD 225
Detailsn/a
Collection Date2008-01-01
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.8726
 
Diffraction Source
SourceSYNCHROTRON
TypeESRF BEAMLINE ID13
SiteESRF
BeamlineID13
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)n/a
Resolution (High)1.80
Resolution (Low)90.00
Number Reflections (All) n/a
Number Reflections (Observed)443
Percent Possible (Observed)85.4
R Merge I (Observed)0.216
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy3.8
 
High Resolution Shell Details
Resolution(High)1.80
Resolution(Low)1.94
Percent Possible(All) 67.00
R Merge I(Observed)0.395
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy1.7
Num Unique Reflections(All)63
 
Resolution(High)1.94
Resolution(Low)2.13
Percent Possible(All) 85.60
R Merge I(Observed)0.327
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy2.3
Num Unique Reflections(All)83
 
Resolution(High)2.13
Resolution(Low)2.44
Percent Possible(All) 78.80
R Merge I(Observed)0.314
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy3.2
Num Unique Reflections(All)89
 
Resolution(High)2.44
Resolution(Low)3.08
Percent Possible(All) 100.00
R Merge I(Observed)0.244
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy5.4
Num Unique Reflections(All)87
 
Resolution(High)3.08
Resolution(Low)90.00
Percent Possible(All) 94.50
R Merge I(Observed)0.197
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy5.1
Num Unique Reflections(All)121
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)1.80
Resolution (Low)20.60
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)433
Number of Reflections (R-Free) 40
Percent Reflections (Observed)86.43
R-Factor (All)n/a
R-Factor (Observed)0.2133
R-Work0.2118
R-Free0.2263
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value20.820
Anisotropic B[1][1]1.00
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-0.04
Anisotropic B[2][3]0.00
Anisotropic B[3][3]-0.95
 
Resolution Shells
Shell Resol (High)1.80
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)4
Number of Reflections (R-Work)87
R-Factor (R-Work)0.382
R-Factor (R-Free)0.330
R-Free Errorn/a
Percent Reflections (Observed)72.22
 
RMS Deviations
Parameter TypeDeviation From Ideal
r_scangle_it1.673
r_scbond_it1.220
r_mcangle_it0.853
r_mcbond_other0.157
r_mcbond_it0.523
r_gen_planes_other0.001
r_gen_planes_refined0.004
r_chiral_restr0.053
r_dihedral_angle_3_deg10.817
r_dihedral_angle_2_deg52.201
r_dihedral_angle_1_deg9.100
r_angle_other_deg0.693
r_angle_refined_deg1.657
r_bond_other_d0.001
r_bond_refined_d0.009
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms48
Nucleic Acid Atoms0
Heterogen Atoms8
Solvent Atoms0
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)DENZO
Data Reduction (data scaling)SCALEPACK
Structure SolutionPHASER
Structure RefinementREFMAC 5.4.0061
 
Software
Classificationreflection data processing
Software NameDENZO
 
Classificationdata scaling
Software NameSCALEPACK
 
Classificationmolecular replacement
Software NamePhaser
Software Version 1.3.2
 
Classificationrefinement
Software NameREFMAC5
 
Classificationdata extraction
Software Namepdb_extract
Software Version 3.10
 
Sequence Chain
A
Sequence
1   IIHFGS