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- PDB-5o7q: Crystal structure of a single chain monellin mutant (Y65R) pH 5.5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o7q | ||||||
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Title | Crystal structure of a single chain monellin mutant (Y65R) pH 5.5 | ||||||
![]() | Monellin chain B,Monellin chain A | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pica, A. / Merlino, A. | ||||||
![]() | ![]() Title: pH driven fibrillar aggregation of the super-sweet protein Y65R-MNEI: A step-by-step structural analysis. Authors: Pica, A. / Leone, S. / Di Girolamo, R. / Donnarumma, F. / Emendato, A. / Rega, M.F. / Merlino, A. / Picone, 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 | ![]() | 93.4 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5o7kC ![]() 5o7lC ![]() 5o7rC ![]() 5o7sC ![]() 2o9uS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 1 - 96 / Label seq-ID: 1 - 96
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Components
#1: Protein | Mass: 11281.872 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: P02882, UniProt: P02881 #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-PEG / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG3350, 0.1 M Bis/Tris pH 5.5, 0.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.72→50 Å / Num. obs: 21238 / % possible obs: 99.7 % / Redundancy: 5.6 % / Net I/σ(I): 9.87 |
Reflection shell | Resolution: 1.72→1.82 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.828 / Num. unique obs: 3364 / CC1/2: 0.886 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2O9U Resolution: 1.72→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.037 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.492 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→50 Å
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Refine LS restraints |
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