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- PDB-4zfw: 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: 4zfw | |||||||||
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Title | Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with galactose. | |||||||||
![]() | (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 | ![]() | 125 KB | Display | ![]() |
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PDB format | ![]() | 94.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4z8sSC ![]() 4z9wC ![]() 4za3C ![]() 4zbvC ![]() 4zfuC ![]() 4zfyC ![]() 4zgrC ![]() 4zlbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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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 , 5 types, 5 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/GLA.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/GLA.gif)
![](data/chem/img/GAL.gif)
#3: 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 |
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#4: Polysaccharide | beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
#7: Sugar | ChemComp-GLA / |
#8: Sugar | ChemComp-GAL / |
-Non-polymers , 2 types, 310 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | GLA B 301 AND GAL B 302 ARE IN ALTERNATE CONFORMATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.27 % |
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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, glycerol |
-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: Apr 30, 2012 |
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: 2.533→142.3 Å / Num. obs: 29954 / % possible obs: 99 % / Redundancy: 6 % / Rsym value: 0.143 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.53→2.67 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Z8S Resolution: 2.54→68.54 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.18 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.247 / 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: 24.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→68.54 Å
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Refine LS restraints |
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