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- PDB-4zfy: Structural studies on a non-toxic homologue of type II RIPs from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zfy | |||||||||
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Title | Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with ALPHA-METHYL-D-GALACTOSIDE | |||||||||
![]() | (rRNA N-glycosidase) x 2 | |||||||||
![]() | HYDROLASE / beta-trefoil / Type II RIPs / Galactose binding lectin | |||||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Chandran, T. / Sharma, A. / Vijayan, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.3 KB | Display | ![]() |
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Full document | ![]() | 782 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4z8sSC ![]() 4z9wC ![]() 4za3C ![]() 4zbvC ![]() 4zfuC ![]() 4zfwC ![]() 4zgrC ![]() 4zlbC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The author states that the symmetry related halves are covalently linked through a disulphide bridge. Therefore, the whole molecule is formally a monomer. |
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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) ![]() |
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#2: Protein | Mass: 29017.416 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 287-547 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/AMG.gif)
![](data/chem/img/AMG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
#5: Sugar | ChemComp-AMG / |
-Non-polymers , 1 types, 114 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % / Description: Orthorhombic crystals, no cryo-protectant |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1M HEPES, 20% w/v PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 18, 2014 |
Radiation | Monochromator: Mirrors POLAR 0.000 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→68.5 Å / Num. obs: 25685 / % possible obs: 97.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.42→2.55 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.8 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Z8S Resolution: 2.42→58.19 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.872 / SU B: 7.028 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.063 / 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: 38.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→58.19 Å
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Refine LS restraints |
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