+Open data
-Basic information
Entry | Database: PDB / ID: 1vbp | |||||||||
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Title | Crystal structure of artocarpin-mannopentose complex | |||||||||
Components | artocarpin | |||||||||
Keywords | PLANT PROTEIN / beta-prism / mannose-specific / lectin / jacalin-like | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Artocarpus integer (campedak) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Jeyaprakash, A.A. / Srivastav, A. / Surolia, A. / Vijayan, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural basis for the carbohydrate specificities of artocarpin: variation in the length of a loop as a strategy for generating ligand specificity Authors: Jeyaprakash, A.A. / Srivastav, A. / Surolia, A. / Vijayan, M. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of artocarpin, a Moraceae lectin with mannose specificity, and its complex with methyl-alpha-D-mannose: implications to the generation of carbohydrate specificity Authors: Pratap, J.V. / Jeyaprakash, A.A. / Rani, P.G. / 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. #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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbp.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbp.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbp ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbp | HTTPS FTP |
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-Related structure data
Related structure data | 1vboC 1j4sS 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16102.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Tissue: seedsSeed / References: UniProt: Q7M1T4 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-SO4 / #5: 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: 12.01 Å3/Da / Density % sol: 89.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Ammonium Sulphate, Phosphate Buffer, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 16, 2003 |
Radiation | Monochromator: OSMIC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. all: 19233 / Num. obs: 19233 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.161 |
Reflection shell | Resolution: 3.5→3.62 Å / Rmerge(I) obs: 0.427 / Num. unique all: 1816 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J4S Resolution: 3.5→19.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 11093993.02 / 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: 10 Å2 / ksol: 0.191774 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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