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Yorodumi- PDB-5y42: Native-crystal structure of three chain non-toxic type II ribosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y42 | ||||||
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Title | Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina | ||||||
Components |
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Keywords | PLANT PROTEIN / beta-trefoil / Lectin | ||||||
Function / homology | Function and homology information rRNA N-glycosylase activity / carbohydrate binding / negative regulation of translation Similarity search - Function | ||||||
Biological species | Trichosanthes anguina (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Chandran, T. / Vijayan, M. | ||||||
Funding support | India, 1items
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Citation | Journal: Glycobiology / Year: 2018 Title: Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study. Authors: Chandran, T. / Sivaji, N. / Surolia, A. / Vijayan, M. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013 Title: The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs. Authors: Sharma, A. / Pohlentz, G. / Bobbili, K.B. / Jeyaprakash, A.A. / Chandran, T. / Mormann, M. / Swamy, M.J. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y42.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y42.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/5y42 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y42 | HTTPS FTP |
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-Related structure data
Related structure data | 5y97C 4hr6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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/peptide | Mass: 4647.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: N-glycosidase domain / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF6, UniProt: U3KRF8*PLUS #2: Protein | Mass: 23128.002 Da / Num. of mol.: 2 / Fragment: UNP residues 48-253 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8 #3: Protein | Mass: 29287.674 Da / Num. of mol.: 2 / Fragment: UNP residues 256-519 / Source method: isolated from a natural source / Source: (natural) Trichosanthes anguina (plant) / References: UniProt: U3KRF8 #4: Sugar | ChemComp-NAG / | #5: 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: 2.77 Å3/Da / Density % sol: 55.58 % / Description: hexagonal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M lithium sulfate monohydrate, 0.1M Tris-Hcl, pH8.5, 30% PEG4000 PH range: 7.4-8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→85.61 Å / Num. obs: 28365 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.198 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4115 / CC1/2: 0.648 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HR6 Resolution: 2.9→85.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.882 / SU B: 20.006 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / 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: 59.753 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→85.01 Å
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Refine LS restraints |
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