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- PDB-8guf: Crystal structure of cyclic B subunit of type II heat labile ente... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8guf | ||||||
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Title | Crystal structure of cyclic B subunit of type II heat labile enterotoxin | ||||||
![]() | (Heat-labile enterotoxin IIB, B chain) x 2 | ||||||
![]() | RECOMBINATION / mucosal adjuvant / B subunit of type II heat labile enterotoxin | ||||||
Function / homology | perturbation of signal transduction in another organism / Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / host cell membrane / toxin activity / extracellular region / Heat-labile enterotoxin IIB, B chain![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, Y.J. / Wu, C.Y. / Sue, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of cyclic B subunit of type II heat labile enterotoxin Authors: Peng, Y.J. / Wu, C.Y. / Sue, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.7 KB | Display | ![]() |
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Full document | ![]() | 471.7 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qb5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 11066.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: linker portion(GSGS) including Gly and Ser, one Serine's electron density is missing Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11066.449 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Sequence details | Structure is a cyclic form. Gly1 is connected to Ser103. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Sodium Citrate, 10% w/v PEG 8000 / PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. obs: 33337 / % possible obs: 97.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.44 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 4 % / Num. unique obs: 3258 / CC1/2: 0.979 / CC star: 0.995 / Rpim(I) all: 0.092 / Rrim(I) all: 0.186 / Χ2: 0.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QB5 Resolution: 1.99→29.42 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.76 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||
Displacement parameters | Biso max: 95.98 Å2 / Biso mean: 26.743 Å2 / Biso min: 13.33 Å2
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Refinement step | Cycle: final / Resolution: 1.99→29.42 Å
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LS refinement shell | Resolution: 1.99→2.041 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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