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- PDB-4iv3: Crystal structure of recombinant foot-and-mouth-disease virus A22... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iv3 | ||||||
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Title | Crystal structure of recombinant foot-and-mouth-disease virus A22-H2093C empty capsid | ||||||
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![]() | VIRUS / ICOSAHEDRAL VIRUS / CAPSIDS / PICORNAVIRUS / APTHOVIRUS / VACCINE | ||||||
Function / homology | ![]() modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Porta, C. / Kotecha, A. / Burman, A. / Jackson, T. / Ren, J. / Loureiro, S. / Jones, I.M. / Fry, E.E. / Stuart, D.I. / Charleston, B. | ||||||
![]() | ![]() Title: Rational engineering of recombinant picornavirus capsids to produce safe, protective vaccine antigen. Authors: Porta, C. / Kotecha, A. / Burman, A. / Jackson, T. / Ren, J. / Loureiro, S. / Jones, I.M. / Fry, E.E. / Stuart, D.I. / Charleston, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.5 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iv1C ![]() 4gh4S 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 23090.180 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 726-936 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 24602.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 287-504 / Mutation: H93C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 24245.127 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 505-725 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 8778.129 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 201-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 4 M ammonium acetate, 100 mM bis-Tris Propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 353968 / % possible obs: 79.7 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.407 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.7 / Num. unique all: 23484 / % possible all: 53.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4GH4 Resolution: 2.9→49.56 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 18170930.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.229 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→49.56 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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