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Open data
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Basic information
Entry | Database: PDB / ID: 4olr | ||||||
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Title | [Leu-5]-Enkephalin mutant - YVVFV | ||||||
![]() | [Leu-5]-Enkephalin mutant - YVVFV | ||||||
![]() | 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 | ![]() | 15.2 KB | Display | ![]() |
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PDB format | ![]() | 10.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391 KB | Display | ![]() |
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Full document | ![]() | 390.9 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 2.9 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,1/2+Y,-Z; 1-X,1/2+Y,-Z; 2-X,1/2+Y,-Z; etc.) |
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Components
#1: Protein/peptide | Mass: 625.755 Da / Num. of mol.: 2 / Fragment: [Leu-5]-Enkephalin / Mutation: G2V,G3V,L5V / Source method: obtained synthetically / Details: synthesized / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MPD / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.58 Å3/Da / Density % sol: 22.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: reservoir contained 15% MPD, 0.1M Sodium Cacodylate, 0.1M Magnesium Acetate, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-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: 1.1→19.02 Å / Num. all: 3191 / Num. obs: 3191 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.65 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.212 / Net I/σ(I): 5.91 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.1→19.02 Å / FOM work R set: 0.8699 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.87 / Stereochemistry target values: ML
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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: 31.87 Å2 / Biso mean: 8.36 Å2 / Biso min: 3.71 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→19.02 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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