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Yorodumi- PDB-2zl7: Atomic resolution structural characterization of recognition of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zl7 | |||||||||
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Title | Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus | |||||||||
Components | 58 kd capsid protein | |||||||||
Keywords | VIRAL PROTEIN / Norovirus / Norwalk virus / HBGA / histo-blood group antigen / carbohydrate / VP1 / P-domain | |||||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Norwalk virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Choi, J.M. / Huston, A.M. / Estes, M.K. / Prasad, B.V.V. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zl7.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zl7.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/2zl7 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/2zl7 | HTTPS FTP |
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-Related structure data
Related structure data | 2zl5C 2zl6C 1ihmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 31529.301 Da / Num. of mol.: 2 / Fragment: P-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk virus / Strain: G.I / Gene: ORF2 / Plasmid: pHisMal-C2ET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83884 #2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)]beta-D-galactopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 741 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 50mM Sodium acetate buffer(pH 4.8), 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å |
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: 1.35→43.6 Å / Num. all: 144576 / Num. obs: 143419 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.66 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ihm Resolution: 1.35→30.07 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.726 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.051 / ESU R Free: 0.052 / 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: 11.818 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→30.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.363→1.398 Å / Total num. of bins used: 20
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