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Yorodumi- PDB-2zmk: Crystl structure of Basic Winged bean lectin in complex with Gal-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zmk | |||||||||
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Title | Crystl structure of Basic Winged bean lectin in complex with Gal-alpha-1,4-Gal-Beta-Ethylene | |||||||||
Components | Basic agglutinin | |||||||||
Keywords | SUGAR BINDING PROTEIN / Legume Lectin / Sugar Specificity / Glycoprotein / Lectin | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | |||||||||
Authors | Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure and sugar-specificity of basic winged-bean lectin: structures of new disaccharide complexes and a comparative study with other known disaccharide complexes of the lectin. Authors: Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. #1: Journal: Proteins / Year: 2007 Title: Generation of blood group specificity: New insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin. Authors: Kulkarni, K.A. / Katiyar, S. / Surolia, A. / Vijayan, M. / Suguna, K. #2: Journal: J.Mol.Biol. / Year: 1998 Title: Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution Authors: Prabu, M.M. / Sankaranarayanan, R. / Puri, K.D. / Sharma, V. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zmk.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zmk.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 2zmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/2zmk ftp://data.pdbj.org/pub/pdb/validation_reports/zm/2zmk | HTTPS FTP |
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-Related structure data
Related structure data | 2zmlC 2zmnC 1wblS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26505.604 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / References: UniProt: O24313 |
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-Sugars , 6 types, 13 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / | #9: Sugar | ChemComp-BMA / | |
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-Non-polymers , 3 types, 179 molecules
#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-CA / #10: 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: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 6-7% PEG 4000, 5% Isopropanol, 20mM PBS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 37178 / Num. obs: 36542 / % possible obs: 98.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 2.8 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.128 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3195 / Rsym value: 0.451 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Starting model: 1WBL Resolution: 2.5→29.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2369758.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.4062 Å2 / ksol: 0.286834 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
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Xplor file |
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