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- PDB-2zl6: Atomic resolution structural characterization of recognition of h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zl6 | |||||||||
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Title | Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus | |||||||||
![]() | 58 kd capsid protein | |||||||||
![]() | VIRAL PROTEIN / Norovirus / Norwalk virus / HBGA / histo-blood group antigen / carbohydrate / VP1 / P-domain | |||||||||
Function / homology | ![]() T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Choi, J.M. / Huston, A.M. / Estes, M.K. / Prasad, B.V.V. | |||||||||
![]() | ![]() Title: Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus Authors: Choi, J.M. / Hutson, A.M. / Estes, M.K. / Prasad, B.V.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.3 KB | Display | ![]() |
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PDB format | ![]() | 108.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.8 KB | Display | ![]() |
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Full document | ![]() | 780.8 KB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zl5C ![]() 2zl7C ![]() 1ihmS C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 31529.301 Da / Num. of mol.: 2 / Fragment: P-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1M Citric Acid(pH 3.8), 0.2M Ammonium Nitrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2007 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→41.73 Å / Num. all: 121668 / Num. obs: 121303 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.38 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.43→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ihm Resolution: 1.43→40.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.075 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.633 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→40.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.467 Å / Total num. of bins used: 20
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