+Open data
-Basic information
Entry | Database: PDB / ID: 5d5g | ||||||
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Title | Structure of colocasia esculenta agglutinin | ||||||
Components | (Tuber agglutinin) x 2 | ||||||
Keywords | SUGAR BINDING PROTEIN / CARBOHYDRATE BINDING / LECTIN / AGGLUTININ / BETA PRISM II | ||||||
Function / homology | Function and homology information response to other organism / D-mannose binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Colocasia esculenta (taro) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Biswas, H. / Chattopadhyaya, R. | ||||||
Funding support | India, 1items
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Citation | Journal: J GLYCOBIO / Year: 2017 Title: Crystal structure Colocasia esculenta tuber agglutinin at 1.74A resolution and its quaternary interactions Authors: Chattopadhyaya, R. / Biswas, H. / Sarkar, A. #1: Journal: J. Biomol. Struct. Dyn. / Year: 2017 Title: Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from alpha 2 beta 2 to unfolded state Authors: Biswas, H. / Chattopadhyaya, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d5g.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d5g.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 5d5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d5g_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 5d5g_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 5d5g_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5d5g_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5g ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5g | HTTPS FTP |
-Related structure data
Related structure data | 3r0eS S: Starting model for refinement |
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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
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 12012.415 Da / Num. of mol.: 2 / Fragment: UNP residues 24-132 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / Plasmid details: local market, food item / Tissue: tuber / References: UniProt: R9RL27 #2: Protein | Mass: 12418.863 Da / Num. of mol.: 2 / Fragment: UNP residues 140-250 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / Plasmid details: local market, food item / Tissue: tuber / References: UniProt: R9RL27 |
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-Non-polymers , 4 types, 141 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-SO4 / | #6: 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: 2.42 Å3/Da / Density % sol: 49.27 % / Description: rectangular plates |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: reservoir included 1.8 M ammonium sulphate and 0.1 M Hepes, pH 6.0; stock protein solution contained 8.1 mg/ml of lectin in 20 mM Tris pH 8.5; protein & reservoir soln mixed in 3:1 ratio at ...Details: reservoir included 1.8 M ammonium sulphate and 0.1 M Hepes, pH 6.0; stock protein solution contained 8.1 mg/ml of lectin in 20 mM Tris pH 8.5; protein & reservoir soln mixed in 3:1 ratio at start and placed on siliconized cover slip Temp details: fluctuated within 5 K |
-Data collection
Diffraction | Mean temperature: 113 K / Ambient temp details: over 2 days, 8 min per frame |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 5, 2014 |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.536→21 Å / Num. obs: 59836 / % possible obs: 83.4 % / Redundancy: 5.61 % / Rmerge(I) obs: 0.38 / Rsym value: 0.38 / Net I/σ(I): 2.7 |
Reflection shell | Resolution: 1.536→1.58 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 0.9 / % possible all: 20 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R0E Resolution: 1.74→20.986 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 60.71 / Stereochemistry target values: ML Details: THERE ARE 7 PROTEIN ATOMS AND 5 WATER MOLECULARS WITH ZERO B FACTORS. AUTHOR HAS CONFIRMED THESE ATOMS AND STATED: 7 PROTEIN ATOMS WITH ZERO B FACTORS AFTER PHENIX REFINEMENT, FOUND TO ...Details: THERE ARE 7 PROTEIN ATOMS AND 5 WATER MOLECULARS WITH ZERO B FACTORS. AUTHOR HAS CONFIRMED THESE ATOMS AND STATED: 7 PROTEIN ATOMS WITH ZERO B FACTORS AFTER PHENIX REFINEMENT, FOUND TO POSSESS QUITE STRONG ELECTRON DENSITIES. THE 5 WATER MOLECULES WITH ZERO TEMPERATURE FACTORS COULD VERY WELL BE SODIUM CATIONS WHICH ARE ISO-ELECTRONIC WITH WATER OXYGEN ATOMS. HOWEVER NA+ IONS SHOULD HAVE HIGHER ELECTRON DENSITIES AT THEIR CENTERS COMPARED TO OXYGEN, DUE TO A HIGHER ATOMIC NUMBER.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.33 Å2 / Biso mean: 19.0229 Å2 / Biso min: 0 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→20.986 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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