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Yorodumi- PDB-5v5h: OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v5h | |||||||||
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Title | OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2 | |||||||||
Components |
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Keywords | hydrolase / transferase / Ovarian Tumor Domain protease / deubiquitinase / ubiquitin variant | |||||||||
Function / homology | Function and homology information RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / metal ion binding Similarity search - Function | |||||||||
Biological species | Crimean-Congo hemorrhagic fever virus synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Khare, B. / Mark, B.L. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: PLoS Pathog. / Year: 2017 Title: Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. Authors: Zhang, W. / Bailey-Elkin, B.A. / Knaap, R.C.M. / Khare, B. / Dalebout, T.J. / Johnson, G.G. / van Kasteren, P.B. / McLeish, N.J. / Gu, J. / He, W. / Kikkert, M. / Mark, B.L. / Sidhu, S.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v5h.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v5h.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 5v5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/5v5h ftp://data.pdbj.org/pub/pdb/validation_reports/v5/5v5h | HTTPS FTP |
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-Related structure data
Related structure data | 5v5gC 5v69C 5v6aC 3pt2S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 19770.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970) Strain: Nigeria/IbAr10200/1970 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase |
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#2: Protein | Mass: 12183.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
-Non-polymers , 4 types, 226 molecules
#3: Chemical | ChemComp-NA / |
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#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-EPE / |
#6: 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: 1.89 Å3/Da / Density % sol: 34.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% (w/v) PEG 4000, 0.2 M CaCl2 and 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.434 Å / Num. obs: 38017 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1876 / CC1/2: 0.79 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PT2 Resolution: 1.5→43.434 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.75 / 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: 1.5→43.434 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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