+Open data
-Basic information
Entry | Database: PDB / ID: 1ax1 | |||||||||
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Title | ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH LACTOSE | |||||||||
Components | LECTIN | |||||||||
Keywords | LECTIN / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Erythrina corallodendron (coral tree) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER FROM PREVIOUSLY DETERMINED, RELATED STRUCTURE / Resolution: 1.95 Å | |||||||||
Authors | Shaanan, B. / Elgavish, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structures of the Erythrina corallodendron lectin and of its complexes with mono- and disaccharides. Authors: Elgavish, S. / Shaanan, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ax1.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ax1.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ax1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1ax1 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1ax1 | HTTPS FTP |
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-Related structure data
Related structure data | 1ax0C 1ax2C 1axyC 1axzC 1lteS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26221.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erythrina corallodendron (coral tree) / References: UniProt: P16404 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
-Non-polymers , 3 types, 150 molecules
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-CA / |
#6: 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: 3.82 Å3/Da / Density % sol: 67.81 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7. | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1993 / Details: FRANCKS MIRRORS (SUPPER 2 X 6 CM MIRRORS) |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 27823 / % possible obs: 91.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.95→2.04 Å / Redundancy: 2 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 5 / Rsym value: 0.263 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 60388 |
Reflection shell | *PLUS Rmerge(I) obs: 0.263 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER FROM PREVIOUSLY DETERMINED, RELATED STRUCTURE Starting model: COMPLEX WITH LACTOSE, PDB ENTRY 1LTE Resolution: 1.95→6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 32.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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