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Yorodumi- PDB-1pxd: Crystal structure of the complex of jacalin with meso-tetrasulpho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pxd | ||||||
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Title | Crystal structure of the complex of jacalin with meso-tetrasulphonatophenylporphyrin. | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / lectin / porphyrin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Artocarpus integer (campedak) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Goel, M. / Anuradha, P. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction. Authors: Goel, M. / Anuradha, P. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Functional equality in the absence of structural similarity: an added dimension to molecular mimicry Authors: Goel, M. / Jain, D. / Kaur, K.J. / Kenoth, R. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pxd.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pxd.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/1pxd ftp://data.pdbj.org/pub/pdb/validation_reports/px/1pxd | HTTPS FTP |
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-Related structure data
Related structure data | 1jacS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14673.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18670 | ||
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#2: Protein/peptide | Mass: 2059.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18673 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Ammonium sulphate and Sodium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 2002 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 23948 / Num. obs: 23948 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 10.8 / Num. unique all: 23948 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JAC Resolution: 1.8→100 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→100 Å
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