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Open data
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Basic information
Entry | Database: PDB / ID: 1ugw | ||||||
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Title | Crystal structure of jacalin- Gal 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 | ![]() | 136.5 KB | Display | ![]() |
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PDB format | ![]() | 106.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.4 KB | Display | ![]() |
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Full document | ![]() | 492.6 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ugxC ![]() 1ugyC ![]() 1uh0C ![]() 1uh1C ![]() 1m26S 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
#1: Protein | Mass: 14643.431 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein/peptide | Mass: 2047.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 14673.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Sugar | ChemComp-GAL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.86 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG 4000, ammonium sulfate, sodium acetate trihydrate, 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: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 91056 / Num. obs: 91056 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.447 / Num. unique all: 8911 / % possible all: 95.8 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. measured all: 350856 |
Reflection shell | *PLUS % possible obs: 95.8 % / Num. unique obs: 8911 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M26 Resolution: 1.7→19.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2109195.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.9882 Å2 / ksol: 0.324271 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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