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- PDB-1fyu: Crystal structure of erythrina corallodendron lectin in hexagonal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fyu | |||||||||
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Title | Crystal structure of erythrina corallodendron lectin in hexagonal crystal form | |||||||||
![]() | LECTIN | |||||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / PROTEIN-CARBOHYDRATE COMPLEX | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Elgavish, S. / Shaanan, B. | |||||||||
![]() | ![]() Title: Chemical characteristics of dimer interfaces in the legume lectin family. Authors: Elgavish, S. / Shaanan, B. #1: ![]() Title: Structure of the Erythrina Corallodendron Lectin and of its Complexes with Mono- and Disaccharides | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.6 KB | Display | ![]() |
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Full document | ![]() | 482.9 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lteS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27919.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Polysaccharide | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, sodium chloride, Hepes buffer, sodium azides, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Elgavish, S., (1998) J. Mol. Biol., 277, 917. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 4, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.16 Å / Num. obs: 26125 / % possible obs: 97.3 % / Redundancy: 8.5 % / Biso Wilson estimate: 43.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 8.6 % / Rsym value: 0.34 / % possible all: 59.9 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 39.16 Å / Redundancy: 8.5 % / Biso Wilson estimate: 43.4 Å2 |
Reflection shell | *PLUS Redundancy: 8.6 % |
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Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: 1LTE.PDB Resolution: 2.6→39.16 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.25 Å2 / ksol: 0.293 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.66 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 6.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.316 / % reflection Rfree: 6.9 % / Rfactor Rwork: 0.237 |