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Yorodumi- PDB-4yn1: THE ATOMIC STRUCTURE OF ANOMALA CUPREA ENTOMOPOXVIRUS (ACEPV) FUS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yn1 | |||||||||
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Title | THE ATOMIC STRUCTURE OF ANOMALA CUPREA ENTOMOPOXVIRUS (ACEPV) FUSOLIN SPINDLES | |||||||||
Components | Fusolin | |||||||||
Keywords | VIRAL PROTEIN / INTRACELLULAR PROTEIN MICRO-CRYSTAL / CHITIN-B DOMAIN / STRUCTURAL PROTEIN / N-GLYCOSYLATION | |||||||||
Function / homology | Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / Fusolin Function and homology information | |||||||||
Biological species | Anomala cuprea entomopoxvirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Chiu, E. / Bunker, R.D. / Metcalf, P. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural basis for the enhancement of virulence by viral spindles and their in vivo crystallization. Authors: Chiu, E. / Hijnen, M. / Bunker, R.D. / Boudes, M. / Rajendran, C. / Aizel, K. / Olieric, V. / Schulze-Briese, C. / Mitsuhashi, W. / Young, V. / Ward, V.K. / Bergoin, M. / Metcalf, P. / Coulibaly, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yn1.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yn1.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yn1_validation.pdf.gz | 739.6 KB | Display | wwPDB validaton report |
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Full document | 4yn1_full_validation.pdf.gz | 740.9 KB | Display | |
Data in XML | 4yn1_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4yn1_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/4yn1 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/4yn1 | HTTPS FTP |
-Related structure data
Related structure data | 4ow5C 4x27C 4x29C 4yn2C 2bemS 4g4t 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41438.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anomala cuprea entomopoxvirus / References: UniProt: O70709 | ||
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 26 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.35 % |
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Crystal grow | Temperature: 300 K / Method: in cell / pH: 7 Details: NATURALLY OCCURRING INTRACELLULAR FUSOLIN MICRO-CRYSTALS WERE PURIFIED FROM EPV-INFECTED LARVAE OF ANOMALA CUPREA MOTHS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62.68 Å / Num. obs: 27160 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 17.5 % / Biso Wilson estimate: 18.27 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BEM Resolution: 1.9→62.68 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.112
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Displacement parameters | Biso mean: 20.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.153 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→62.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.98 Å / Total num. of bins used: 13
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