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- PDB-4z9w: 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: 4z9w | |||||||||
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Title | Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-2 | |||||||||
![]() | (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 | ![]() | 131 KB | Display | ![]() |
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PDB format | ![]() | 99.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 955.3 KB | Display | ![]() |
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Full document | ![]() | 956.9 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4z8sSC ![]() 4za3C ![]() 4zbvC ![]() 4zfuC ![]() 4zfwC ![]() 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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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 , 3 types, 5 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/BMA.gif)
#3: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[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 | #6: Sugar | ChemComp-BMA / | |
-Non-polymers , 2 types, 553 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % / Description: orthorhombic |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1 M HEPES, 20% w/v PEG 10000, No-cryo protectant used |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011 |
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 | Resolution: 1.77→139.32 Å / Num. all: 73778 / Num. obs: 73778 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.129 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Z8S Resolution: 1.77→91.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.366 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / 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: 23.547 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→91.18 Å
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Refine LS restraints |
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