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Yorodumi- PDB-4d9j: Structure of a 16 nm protein cage designed by fusing symmetric ol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d9j | ||||||
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Title | Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains | ||||||
Components | Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1 | ||||||
Keywords | DE NOVO PROTEIN / protein design / bionanotechnology / protein assembly / symmetry / biomaterials | ||||||
Function / homology | Function and homology information Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / antibiotic biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / viral budding from plasma membrane / peroxidase activity / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Streptomyces aureofaciens (bacteria) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.92 Å | ||||||
Authors | Lai, Y.-T. / Cascio, D. / Yeates, T.O. | ||||||
Citation | Journal: Science / Year: 2012 Title: Structure of a 16-nm cage designed by using protein oligomers. Authors: Lai, Y.T. / Cascio, D. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d9j.cif.gz | 958.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d9j.ent.gz | 805.5 KB | Display | PDB format |
PDBx/mmJSON format | 4d9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d9j_validation.pdf.gz | 540.9 KB | Display | wwPDB validaton report |
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Full document | 4d9j_full_validation.pdf.gz | 589.8 KB | Display | |
Data in XML | 4d9j_validation.xml.gz | 165.6 KB | Display | |
Data in CIF | 4d9j_validation.cif.gz | 220.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/4d9j ftp://data.pdbj.org/pub/pdb/validation_reports/d9/4d9j | HTTPS FTP |
-Related structure data
Related structure data | 3vdxSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50264.414 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria), (gene. exp.) Influenza A virus Strain: A/Puerto Rico/8/1934 H1N1 / Gene: bpoA2, BROMOPEROXIDASE A2, M, M1 Matrix / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P29715, UniProt: P03485, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.3 Details: 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.92→19.893 Å / Num. obs: 58471 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 7.097 % / Biso Wilson estimate: 99.433 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3VDX Resolution: 3.92→19.893 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7759 / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0.27 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.45 Å2 / Biso mean: 54.1233 Å2 / Biso min: 17.38 Å2
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Refinement step | Cycle: LAST / Resolution: 3.92→19.893 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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