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- PDB-1ugx: Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ugx | |||||||||
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Title | Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complex | |||||||||
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![]() | SUGAR BINDING PROTEIN / All beta sheet protein / Beta-prism I fold / Galactose-specific | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M. | |||||||||
![]() | ![]() Title: Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study Authors: Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M. #1: ![]() Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes Authors: Jeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M. #2: ![]() Title: A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold Authors: Sankaranarayanan, R. / sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / 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 | ![]() | 45.5 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 14643.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2059.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
#3: Polysaccharide | beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside![]() Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 59.69 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG 4000, NaCl, sodium azide, Phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→30 Å / Num. all: 27418 / Num. obs: 27418 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.163 / Num. unique all: 2452 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Num. measured all: 139555 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 83 % / Num. unique obs: 2452 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.0741 Å2 / ksol: 0.353446 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→26.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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