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Yorodumi- PDB-1ugy: Crystal structure of jacalin- mellibiose (Gal-alpha(1-6)-Glc) complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ugy | |||||||||
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Title | Crystal structure of jacalin- mellibiose (Gal-alpha(1-6)-Glc) complex | |||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / All beta sheets protein / Beta-prism I fold / Gal specific | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Artocarpus integer (campedak) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M. | |||||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 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: Journal: J.Mol.Biol. / Year: 2002 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: Journal: Nat.Struct.Biol. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ugy.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ugy.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ugy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/1ugy ftp://data.pdbj.org/pub/pdb/validation_reports/ug/1ugy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Agglutinin alpha ... , 2 types, 4 molecules AGCE
#1: Protein | Mass: 14643.431 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seedsSeed / References: UniProt: P18670 #3: Protein | Mass: 14673.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seedsSeed / References: UniProt: P18670 |
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-Protein/peptide / Non-polymers , 2 types, 259 molecules BDFH
#2: Protein/peptide | Mass: 2047.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seedsSeed / References: UniProt: P18673 #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 4 molecules
#4: Polysaccharide | #5: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Details
Sequence details | THERE ARE REPORTED EVIDENCES FOR THE SEQUENCE HETEROGENI |
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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: 3.06 Å3/Da / Density % sol: 59.47 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: Osmic mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 32331 / Num. obs: 32331 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.138 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.4 / Num. unique all: 3044 / % possible all: 91.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 106303 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 91.1 % / Num. unique obs: 3044 / Rmerge(I) obs: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.74 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1643950.95 / 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: 40.0888 Å2 / ksol: 0.310732 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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