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Yorodumi- PDB-4r6p: Jacalin-carbohydrate interactions. Distortion of the ligand as a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r6p | ||||||
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Title | Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity. | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / Galactose specific lectin / beta-prism I fold / post translational proteolysis / T-antigen binding protein / Plant lectins / Galactose | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Artocarpus integer (campedak) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Abhinav, K.V. / Sharma, K. / Swaminathan, C.P. / Surolia, A. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity. Authors: Abhinav, K.V. / Sharma, K. / Swaminathan, C.P. / Surolia, A. / Vijayan, M. #1: 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. #2: 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. / Geetha Rani, P. / Banuprakash Reddy, G. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M. #3: 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. #4: Journal: J.Mol.Biol. / Year: 2005 Title: Structural basis for the energetics of jacalin-sugar interactions: promiscuity versus specificity. Authors: Arockia Jeyaprakash, A. / Jayashree, G. / Mahanta, S.K. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M. #5: Journal: Biochem.J. / Year: 2002 Title: Structural basis for the unusual carbohydrate-binding specificity of jacalin towards galactose and mannose. Authors: Bourne, Y. / Astoul, C.H. / Zamboni, V. / Peumans, W.J. / Menu-Bouaouiche, L. / Van Damme, E.J. / Barre, A. / Rouge, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r6p.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r6p.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r6p ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r6p | HTTPS FTP |
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-Related structure data
Related structure data | 4r6nC 4r6oC 4r6qC 4r6rC 1ku8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 9 molecules ACEGBDFH
#1: Protein | Mass: 14673.479 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18670 #2: Protein/peptide | Mass: 1944.170 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-20 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18673 #6: Sugar | ChemComp-GAL / | |
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-Non-polymers , 4 types, 481 molecules
#3: Chemical | ChemComp-IPA / #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-ZZ1 / | #7: 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: 2.12 Å3/Da / Density % sol: 42.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15% PEG 8000, 0.1M HEPES, pH 7.4, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2013 / Details: Bent collimating mirror and toroid | ||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→60 Å / Num. all: 60267 / Num. obs: 60267 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.077 / Net I/σ(I): 11.5 | ||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KU8 Resolution: 1.7→30.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.349 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 26.714 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30.63 Å
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Refine LS restraints |
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