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Open data
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Basic information
Entry | Database: PDB / ID: 5aoo | ||||||
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Title | X-ray structure of a human Kobuvirus: Aichi virus A (AiV) | ||||||
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![]() | VIRUS / AICHI VIRUS / KOBUVIRUS / PICORNAVIRUS / ACUTE GASTROENTERISIS / ICOSAHEDRAL CAPSID / FULL VIRUS PARTICLE | ||||||
Function / homology | ![]() host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / RNA helicase ...host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sabin, C. / Palkova, L. / Plevka, P. | ||||||
![]() | ![]() Title: The Use of Noncrystallographic Symmetry Averaging to Solve Structures from Data Affected by Perfect Hemihedral Twinning Authors: Sabin, C. / Plevka, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.7 KB | Display | ![]() |
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PDB format | ![]() | 123.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bevS 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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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | |||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 27194.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 38950.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 24082.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.78 % Description: FOR TWINNING ANALYSES AND CALCULATION OF INITIAL ROTATION FUNCTIONS THE AIV DIFFRACTION IMAGES WERE PROCESSED IN SPACEGROUP I23 TO 2.3 ANGSTROM RESOLUTION IN PROGRAM XDS. HOWEVER, SINCE ...Description: FOR TWINNING ANALYSES AND CALCULATION OF INITIAL ROTATION FUNCTIONS THE AIV DIFFRACTION IMAGES WERE PROCESSED IN SPACEGROUP I23 TO 2.3 ANGSTROM RESOLUTION IN PROGRAM XDS. HOWEVER, SINCE THE DATA ANALYSIS REVEALED THAT THE CRYSTAL WAS PERFECTLY HEMIHEDRALLY TWINNED THE IMAGES WERE RE-PROCESSED IN SPACE GROUP I432. TAKING ADVANTAGE OF THE HIGHER SYMMETRY ALLOWED US TO OBTAIN DATASET THAT WAS MORE THAN 90 PERCENT COMPLETE FROM FIRST 160 DIFFRACTION IMAGES, CORRESPONDING TO 16 DEG ROTATION RANGE, AND THE DATA COULD BE PROCESSED TO 2.1 ANGSTROM RESOLUTION. SUBSEQUENTLY, THE DATA WERE EXPANDED FROM I432 TO I23 USING THE PROGRAM SFTOOLS FROM CCP4 PACKAGE. |
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Crystal grow | pH: 7.5 Details: 0.05M CADMIUM SULFATE 0.1M HEPES PH 7.5 1.0M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2014 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSING |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→71.46 Å / Num. obs: 186646 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.1 / % possible all: 83.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BEV Resolution: 2.1→71.46 Å / Stereochemistry target values: ENGH & HUBER /
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Displacement parameters | Biso mean: 22.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→71.46 Å
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Refine LS restraints |
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Xplor file |
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