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Yorodumi- PDB-4za3: Structural studies on a non-toxic homologue of type II RIPs from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4za3 | |||||||||
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Title | Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-3 | |||||||||
Components | (rRNA N-glycosidaseRRNA N-glycosylase) x 2 | |||||||||
Keywords | HYDROLASE / beta-trefoil / Type II RIPs / Galactose specific lectin | |||||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | |||||||||
Biological species | Momordica charantia (bitter melon) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | |||||||||
Authors | Chandran, T. / Sharma, A. / Vijayan, M. | |||||||||
Funding support | India, 1items
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Citation | Journal: J.Biosci. / Year: 2015 Title: Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure. Authors: Chandran, T. / Sharma, A. / Vijayan, M. #1: Journal: Acta Crystallogr. F Biol. Crystallogr. / Year: 2010 Title: Crystallization and preliminary X-ray studies of a galactose-specific lectin from the seeds of bitter gourd (Momordica charantia). Authors: Sharma, A. / Pohlentz, G. / Bobbili, K.B. / Jeyaprakash, A.A. / Chandran, T. / Mormann, M. / Swamy, M.J. / Vijayan, M. #2: 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 | 4za3.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4za3.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 4za3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/4za3 ftp://data.pdbj.org/pub/pdb/validation_reports/za/4za3 | HTTPS FTP |
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-Related structure data
Related structure data | 4z8sSC 4z9wC 4zbvC 4zfuC 4zfwC 4zfyC 4zgrC 4zlbC 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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Unit cell |
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Details | The symmetry related halves are covalently linked through a disulphide bridge. Therefore, the whole molecule is formally a monomer. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 27642.234 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-270 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: B7X8M2, rRNA N-glycosylase |
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#2: Protein | Mass: 28903.309 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 288-547 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: B7X8M2, rRNA N-glycosylase |
-Sugars , 4 types, 4 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 577 molecules
#6: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-GOL / | #9: 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: 3.16 Å3/Da / Density % sol: 61.11 % / Description: orthorhombic |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1M HEPES, 25% w/v PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.4 % / Number: 568970 / Rsym value: 0.07 / D res high: 1.674 Å / D res low: 32.495 Å / Num. obs: 88689 / % possible obs: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.67→32.5 Å / Num. obs: 88689 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.346 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z8S Resolution: 1.67→32.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.42 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 20.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→32.5 Å
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Refine LS restraints |
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