+Open data
-Basic information
Entry | Database: PDB / ID: 1is5 | ||||||
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Title | Ligand free Congerin II | ||||||
Components | Congerin II | ||||||
Keywords | SUGAR BINDING PROTEIN / BETA SANDWICH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Conger myriaster (whitespotted conger) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shirai, T. / Matsui, Y. / Shionyu-Mitsuyama, C. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2002 Title: Crystal structure of a conger eel galectin (congerin II) at 1.45 A resolution: Implication for the accelerated evolution of a new ligand-binding site following gene duplication Authors: Shirai, T. / Matsui, Y. / Shionyu-Mitsuyama, C. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1is5.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1is5.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1is5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/1is5 ftp://data.pdbj.org/pub/pdb/validation_reports/is/1is5 | 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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Details | The second part of the biological assembly is generated by the two fold axis : y, x, -z+1. |
-Components
#1: Protein | Mass: 15354.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Conger myriaster (whitespotted conger) / Plasmid: pTV118N / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9YIC2 |
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#2: 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: 2.47 Å3/Da / Density % sol: 50.13 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium sulfate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. all: 10908 / Num. obs: 10908 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 23.5 / Num. unique all: 1058 / % possible all: 98.5 |
Reflection | *PLUS Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 98.5 % / Num. unique obs: 1058 / Rmerge(I) obs: 0.086 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Congerin II Lactose and MES complex Resolution: 2→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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Refinement | *PLUS Rfactor all: 0.171 / Rfactor obs: 0.17 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.168 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 / Rfactor Rwork: 0.182 |