+Open data
-Basic information
Entry | Database: PDB / ID: 4m9i | ||||||
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Title | A125C NS2B-NS3 protease from dengue virus at pH 5.5 | ||||||
Components | NS2B-NS3 protease | ||||||
Keywords | VIRAL PROTEIN / serine protease / allosteric inhibition / dengue virus protease / trypsin-like protease / conformational flexibility / viral protease | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Yildiz, M. / Hardy, J.A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Allosteric Inhibition of the NS2B-NS3 Protease from Dengue Virus. Authors: Yildiz, M. / Ghosh, S. / Bell, J.A. / Sherman, W. / Hardy, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m9i.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m9i.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 4m9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m9i_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
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Full document | 4m9i_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 4m9i_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4m9i_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m9i ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m9i | HTTPS FTP |
-Related structure data
Related structure data | 4m9fC 4m9kC 4m9mC 4m9tC 2fomS 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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Unit cell |
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-Components
#1: Protein | Mass: 26360.479 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1394-1440, 1476-1660 / Mutation: A125C Source method: isolated from a genetically manipulated source Details: We ligated a synthetic gene encoding 6xHis(tag), NS2B region (43-95), GlyGlyGly GlySerGlyGlyGlyGly(linker, NS3 (1-185) Source: (gene. exp.) Dengue virus 2 / Gene: NS2B-NS3 / Plasmid: DVP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q91H74, UniProt: P12823*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS PROTEIN IS A FUSION PROTEIN CONTAINING RESIDUES 43-95 FROM DENGUE VIRUS NS2B, A GGGGSGGGG ...THIS PROTEIN IS A FUSION PROTEIN CONTAINING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 40% PEG200, 0.1 M Acetic acid, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2011 |
Radiation | Monochromator: SI (111) Channel Cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→50 Å / Num. all: 8544 / Num. obs: 8116 / % possible obs: 98.8 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 3.5 / Redundancy: 3.2 % / Biso Wilson estimate: 62.7 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.37→2.41 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.04 / Num. unique all: 817 / Rsym value: 0.539 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FOM Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.505 / SU ML: 0.201 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2.1 / σ(I): 3.8 / ESU R: 0.49 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.664 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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