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Open data
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Basic information
Entry | Database: PDB / ID: 3a5p | ||||||
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Title | Crystal structure of hemagglutinin | ||||||
![]() | Haemagglutinin I | ||||||
![]() | SUGAR BINDING PROTEIN / lectin | ||||||
Function / homology | Tumour Suppressor Smad4 - #70 / Hemagglutinin I / Hemagglutinin I / Tumour Suppressor Smad4 / Sandwich / Mainly Beta / Haemagglutinin I![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Watanabe, N. / Sakai, N. / Nakamura, T. / Nabeshima, Y. / Kouno, T. / Mizuguchi, M. / Kawano, K. | ||||||
![]() | ![]() Title: The Structure of Physarum polycephalum hemagglutinin I suggests a minimal carbohydrate recognition domain of legume lectin fold Authors: Kouno, T. / Watanabe, N. / Sakai, N. / Nakamura, T. / Nabeshima, Y. / Morita, M. / Mizuguchi, M. / Aizawa, T. / Demura, M. / Imanaka, T. / Tanaka, I. / Kawano, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.5 KB | Display | ![]() |
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PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.9 KB | Display | ![]() |
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Full document | ![]() | 434 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 41.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10900.101 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG3350, 150mM NaI, pH 6.5, vapour diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 8, 2006 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.502 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 40006 / % possible obs: 99.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 21.97 Å2 / Rsym value: 0.03 / Net I/σ(I): 49.4 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 11 / Rsym value: 0.161 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: initial model determined by SAD Resolution: 1.82→30.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.423 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.48 Å2 / Biso mean: 23.215 Å2 / Biso min: 11.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1574 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.1514 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→30.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.819→1.867 Å / Total num. of bins used: 20
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