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Open data
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Basic information
Entry | Database: PDB / ID: 3fva | ||||||
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Title | NNQNTF segment from elk prion | ||||||
![]() | Major prion protein | ||||||
![]() | PROTEIN FIBRIL / amyloid-like protofibril / Cell membrane / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane / Prion | ||||||
Function / homology | ![]() side of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / plasma membrane Similarity search - Function | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Apostol, M.I. / Eisenberg, D. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 8.5 KB | Display | ![]() |
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PDB format | ![]() | 5.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.4 KB | Display | ![]() |
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Full document | ![]() | 369.4 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 2.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fodC ![]() 3fpoC ![]() 3fr1C ![]() 3fthC ![]() 3ftkC ![]() 3ftlC ![]() 3ftrC ![]() 4np8C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | Authors 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 | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.248 Å3/Da / Density % sol: 1.417 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 13, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.946496 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 11.11 Å2 / Biso mean: 0.702 Å2 / Biso min: 0 Å2
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Refinement step | Cycle: LAST / Resolution: 1.458→21.03 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.458→1.496 Å / Total num. of bins used: 20
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