+Open data
-Basic information
Entry | Database: PDB / ID: 7eua | ||||||
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Title | X-ray structure of a P93A Monellin mutant | ||||||
Components | Monellin | ||||||
Keywords | PLANT PROTEIN / W4Y / F19W / P93A / X-ray crystal structure | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Manjula, R. / Bhatia, S. / Jayant, B. / Ramaswamy, S. / Gosavi, S. | ||||||
Citation | Journal: To Be Published Title: X-ray structure of a P93A Monellin mutant Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eua.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eua.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 7eua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/7eua ftp://data.pdbj.org/pub/pdb/validation_reports/eu/7eua | HTTPS FTP |
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-Related structure data
Related structure data | 2o9uS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11409.012 Da / Num. of mol.: 1 / Mutation: W4Y, F19W, P93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | The complete sequence of single chain Monellin has been deposited to NCBI with accession code ...The complete sequence of single chain Monellin has been deposited to NCBI with accession code AFF58925. W4Y, F19W, P93A represent mutations. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, 30% PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 29, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.43→64.94 Å / Num. obs: 3068 / % possible obs: 93.9 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Net I/σ(I): 14.3 / Num. measured all: 18402 / Scaling rejects: 14 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O9U Resolution: 2.43→32.47 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 19.26 / 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: 74.74 Å2 / Biso mean: 29.0322 Å2 / Biso min: 11.9 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.43→32.47 Å
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