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Yorodumi- PDB-1rit: Crystal structure of Peanut lectin in complex with meso-tetrasulp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rit | |||||||||
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Title | Crystal structure of Peanut lectin in complex with meso-tetrasulphonatophenylporphyrin and lactose | |||||||||
Components | Galactose-binding lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Arachis hypogaea (peanut) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Goel, M. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal structures of the PNA-porphyrin complex in the presence and absence of lactose: mapping the conformational changes on lactose binding, interacting surfaces, and supramolecular aggregations. Authors: Goel, M. / Damai, R.S. / Sethi, D.K. / 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 | 1rit.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rit.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1rit ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1rit | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 6 molecules ABCD
#1: Protein | Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872 #2: Polysaccharide | |
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-Non-polymers , 4 types, 61 molecules
#3: Chemical | ChemComp-SFP / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MN / #6: 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: 3.72 Å3/Da / Density % sol: 66.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Ammonium sulphate, Sodium Chloride, Phosphate buffe, 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: Oct 8, 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: 2.85→100 Å / Num. all: 33919 / Num. obs: 33919 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.85→2.95 Å / Rmerge(I) obs: 0.761 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→100 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.85→100 Å
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LS refinement shell | Resolution: 2.85→2.87 Å / Rfactor Rfree: 0.381 / Rfactor Rwork: 0.456 |