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- PDB-3q39: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q39 | |||||||||
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Title | Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type H2 (diglycan) | |||||||||
![]() | Capsid protein | |||||||||
![]() | VIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA) | |||||||||
Function / homology | ![]() Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hansman, G.S. / Biertumpfel, C. / Chen, L. / Georgiev, I. / McLellan, J.S. / Katayama, K. / Kwong, P.D. | |||||||||
![]() | ![]() Title: Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. Authors: Hansman, G.S. / Biertumpfel, C. / Georgiev, I. / McLellan, J.S. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.6 KB | Display | ![]() |
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PDB format | ![]() | 217.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.6 KB | Display | ![]() |
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Full document | ![]() | 800 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3onuSC ![]() 3onyC ![]() 3pa1C ![]() 3pa2C ![]() 3q38C ![]() 3q3aC ![]() 3q6qC ![]() 3q6rC ![]() 3r6jC ![]() 3r6kC 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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Details | Asymmetric unit is also biological unit. |
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Components
#1: Protein | Mass: 34804.953 Da / Num. of mol.: 2 / Fragment: unp reisdues 224-538 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-IMD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Imidazol pH 6.5, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→28.24 Å / Num. all: 190028 / Num. obs: 190028 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 9.7 Å2 / Rsym value: 0.052 / Net I/σ(I): 16.12 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 14021 / Rsym value: 0.674 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ONU Resolution: 1.25→28.24 Å / SU ML: 0.13 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.176 Å2 / ksol: 0.355 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.617 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→28.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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