[English] 日本語
Yorodumi- PDB-1ws5: Crystal structure of Jacalin-Me-alpha-Mannose complex: Promiscuit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ws5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Jacalin-Me-alpha-Mannose complex: Promiscuity vs Specificity | ||||||
Components |
| ||||||
Keywords | SUGAR BINDING PROTEIN / Beta-prism-I fold / Post translational proteolysis / laectin / galactose-specific | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Artocarpus integer (campedak) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Jeyaprakash, A.A. / Jayashree, G. / Mahanta, S.K. / Sekar, K. / Surolia, A. / Vijayan, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural basis for the energetics of jacalin-sugar interactions: promiscuity versus specificity Authors: Jeyaprakash, A.A. / Jayashree, G. / Mahanta, S.K. / Swaminathan, C.P. / Sekar, K. / 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ws5.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ws5.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ws5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/1ws5 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/1ws5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ws4C 1ugwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#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 #2: Protein/peptide | Mass: 2031.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seedsSeed / References: UniProt: P18673 #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 #4: Sugar | ChemComp-MMA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.2 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 25% PEG 4K, 0.2M ammonium sulphate, 0.1M sodium acetate trihydrate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 2004 / Details: osmic mirrors |
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: 1.9→30 Å / Num. all: 65880 / Num. obs: 65146 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.365 / Num. unique all: 6356 / % possible all: 97.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1UGW Resolution: 1.9→26.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2128007.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7302 Å2 / ksol: 0.329859 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→26.58 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|