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Yorodumi- PDB-5z1p: Structural basis of the improved sweetness and stability of the s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z1p | ||||||
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Title | Structural basis of the improved sweetness and stability of the single-chain sweet-tasting protein monellin (MNEI) | ||||||
Components | Monellin chain B,Monellin chain A | ||||||
Keywords | PLANT PROTEIN / monellin | ||||||
Function / homology | Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B Function and homology information | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Liu, B. | ||||||
Citation | Journal: Biochimie / Year: 2018 Title: Structure basis of the improved sweetness and thermostability of a unique double-sites single-chain sweet-tasting protein monellin (MNEI) mutant Authors: Zhao, M. / Xu, X. / Liu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z1p.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z1p.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 5z1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/5z1p ftp://data.pdbj.org/pub/pdb/validation_reports/z1/5z1p | HTTPS FTP |
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-Related structure data
Related structure data | 1iv7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 11346.002 Da / Num. of mol.: 4 / Mutation: E2N, E23A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Sodium Aceteta, 0.1M Tris PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 29868 / % possible obs: 96.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.081 / Rsym value: 0.152 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.418 / Num. unique obs: 1400 / Rpim(I) all: 0.252 / Rsym value: 0.452 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IV7 Resolution: 1.89→40.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.503 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.069 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→40.93 Å
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Refine LS restraints |
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