+Open data
-Basic information
Entry | Database: PDB / ID: 8jz1 | |||||||||
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Title | Crystal structure of a single-chain monellin mutant C41V | |||||||||
Components | Monellin chain B,Monellin chain A | |||||||||
Keywords | PLANT PROTEIN / Sweet protein | |||||||||
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: 1.239 Å | |||||||||
Authors | Yasui, N. / Ohnuma, K. / Yamashita, A. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Protein J. / Year: 2023 Title: Investigating the Effect of Substituting a Single Cysteine Residue on the Thermal Stability of an Engineered Sweet Protein, Single-Chain Monellin. Authors: Ohnuma, K. / Yamashita, A. / Yasui, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jz1.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jz1.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 8jz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/8jz1 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jz1 | HTTPS FTP |
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-Related structure data
Related structure data | 8jz0C 1molS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11223.744 Da / Num. of mol.: 2 / Mutation: C41V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 6.0, 35% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.239→50 Å / Num. obs: 81703 / % possible obs: 84.6 % / Redundancy: 3.4 % / CC1/2: 0.988 / Net I/σ(I): 19.04 |
Reflection shell | Resolution: 1.24→1.3 Å / Num. unique obs: 6581 / CC1/2: 0.878 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MOL Resolution: 1.239→46 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.25 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.239→46 Å
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Refine LS restraints |
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LS refinement shell |
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