+Open data
-Basic information
Entry | Database: PDB / ID: 4zpd | ||||||
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Title | Coxsackievirus B3 Polymerase - A345V mutant | ||||||
Components | RNA-directed RNA polymerase | ||||||
Keywords | TRANSFERASE / RNA-dependent RNA polymerase / TRANSCRIPTION | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Coxsackievirus B3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.797 Å | ||||||
Authors | Peersen, O.B. / McDonald, S.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Design of a Genetically Stable High Fidelity Coxsackievirus B3 Polymerase That Attenuates Virus Growth in Vivo. Authors: McDonald, S. / Block, A. / Beaucourt, S. / Moratorio, G. / Vignuzzi, M. / Peersen, O.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zpd.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zpd.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zpd_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 4zpd_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 4zpd_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 4zpd_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/4zpd ftp://data.pdbj.org/pub/pdb/validation_reports/zp/4zpd | HTTPS FTP |
-Related structure data
Related structure data | 4zp6C 4zp7C 4zp8C 4zp9C 4zpaC 4zpbC 4zpcC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 52505.098 Da / Num. of mol.: 1 / Mutation: A345V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus B3 / Plasmid: pET26/Ub / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5UEA2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.085 M Tris, 1.2 M Ammonium Sulfate , 25% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.797→58.957 Å / Num. obs: 144417 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.108 / Χ2: 1.029 / Net I/σ(I): 14.45 / Num. measured all: 1035067 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.797→58.957 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.797→58.957 Å
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Refine LS restraints |
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LS refinement shell |
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