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Open data
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Basic information
Entry | Database: PDB / ID: 4onk | ||||||
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Title | [Leu-5]-Enkephalin mutant - YVVFL | ||||||
![]() | [Leu-5]-Enkephalin mutant - YVVFL | ||||||
![]() | PROTEIN FIBRIL / amyloid-like protofibril | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sangwan, S. / Eisenberg, D. / Sawaya, M.R. / Do, T.D. / Bowers, M.T. / Lapointe, N.E. / Teplow, D.B. / Feinstein, S.C. | ||||||
![]() | ![]() Title: Factors that drive Peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants. Authors: Do, T.D. / LaPointe, N.E. / Sangwan, S. / Teplow, D.B. / Feinstein, S.C. / Sawaya, M.R. / Eisenberg, D.S. / Bowers, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 9.9 KB | Display | ![]() |
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PDB format | ![]() | 5.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.9 KB | Display | ![]() |
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Full document | ![]() | 402.9 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 | The biological unit is a pair of beta sheets. One sheet is constructed from chains A and B with unit cell translations along the a direction (i.e. X+1,Y,Z; X+2,Y,Z; X+3,Y,Z, etc.). The second sheet is constructed from X,Y+1,Z; X+1,Y+1,Z; X+2,Y+1,Z; etc.). |
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Components
#1: Protein/peptide | Mass: 639.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: reservoir contained 25% PEG 3350, 0.2M Potassium Thiocyanate, vapor diffusion, hanging drop, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→100 Å / Num. all: 537 / Num. obs: 537 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 8.11 Å2 / Rmerge(I) obs: 0.151 / Χ2: 3.634 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ideal beta strand with sequence AVVAA Resolution: 1.9→9.278 Å / FOM work R set: 0.8404 / SU ML: 0.29 / σ(F): 35.13 / Phase error: 23.66 / Stereochemistry target values: LS_WUNIT_K1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||
Displacement parameters | Biso max: 22.76 Å2 / Biso mean: 14.15 Å2 / Biso min: 8.29 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→9.278 Å /
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.9003 Å / Total num. of bins used: 1
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