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- PDB-4en8: Crystal structure of HA70 (HA3) subcomponent of Clostridium botul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4en8 | |||||||||
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Title | Crystal structure of HA70 (HA3) subcomponent of Clostridium botulinum type C progenitor toxin in complex with alpha 2-6-sialyllactose | |||||||||
![]() | (Hemagglutinin components HA-22/23/53) x 2 | |||||||||
![]() | SUGAR BINDING PROTEIN / Carbohydrate/Sugar Binding | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Yamashita, S. / Yoshida, H. / Tonozuka, T. / Nishikawa, A. / Kamitori, S. | |||||||||
![]() | ![]() Title: Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides Authors: Yamashita, S. / Yoshida, H. / Uchiyama, N. / Nakakita, Y. / Nakakita, S. / Tonozuka, T. / Oguma, K. / Nishikawa, A. / Kamitori, S. #1: ![]() Title: Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin Authors: Nakamura, T. / Kotani, M. / Tonozuka, T. / Ide, A. / Oguma, K. / Nishikawa, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.7 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 823 KB | Display | ![]() |
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Full document | ![]() | 841.8 KB | Display | |
Data in XML | ![]() | 29.6 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4en6C ![]() 4en7C ![]() 4en9C ![]() 2zs6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26050.873 Da / Num. of mol.: 1 / Fragment: HA22-23(HA3a) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 47333.520 Da / Num. of mol.: 1 / Fragment: HA53(HA3b) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 6'-sialyl-lactose | ||
#4: Chemical | ChemComp-MRD / ( #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.99 Å3/Da / Density % sol: 75.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 12%(v/v) 2-methyl-2,4-pentendiol, 20mM CaCl2, 100mM sodium acetate, pH 4.6, VAPOR 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: Apr 21, 2011 |
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→50 Å / Num. all: 44625 / Num. obs: 44625 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1460 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZS6 Resolution: 2.6→34.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1866000.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.389 Å2 / ksol: 0.338268 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→34.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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