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Yorodumi- PDB-3zfq: Crystal structure of product-like, processed N-terminal protease ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zfq | ||||||
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Title | Crystal structure of product-like, processed N-terminal protease Npro with mercury | ||||||
Components | N-TERMINAL PROTEASE NPRO | ||||||
Keywords | HYDROLASE / AUTO-PROCESSING CYSTEINE PROTEASE / VIRAL PROTEASE / IN CIS- CLEAVAGE / HYDROXIDE-DEPENDENT CATALYSIS / AUTO-PROTEOLYSIS / IMMUNE MODULATION / HOST-PATHOGEN INTERACTION / CONVERGENT EVOLUTION | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral protein processing / cysteine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | PESTIVIRUS STRAIN D32/00_HOBI | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Zogg, T. / Sponring, M. / Schindler, S. / Koll, M. / Schneider, R. / Brandstetter, H. / Auer, B. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Crystal Structures of the Viral Protease Npro Imply Distinct Roles for the Catalytic Water in Catalysis Authors: Zogg, T. / Sponring, M. / Schindler, S. / Koll, M. / Schneider, R. / Brandstetter, H. / Auer, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zfq.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zfq.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/3zfq ftp://data.pdbj.org/pub/pdb/validation_reports/zf/3zfq | HTTPS FTP |
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-Related structure data
Related structure data | 3zfnSC 3zfoC 3zfpC 3zfrC 3zftC 3zfuC 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: 16558.031 Da / Num. of mol.: 1 / Fragment: NPRO, RESIDUES 22-168 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PESTIVIRUS STRAIN D32/00_HOBI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5L4B1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-SGM / |
#3: Chemical | ChemComp-HG / |
#4: 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 100MM NAACETATE, PH 8.5 50% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→10 Å / Num. obs: 4228 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZFN Resolution: 2.65→10 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.833 / SU B: 11.742 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-150 DISORDERED
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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: 13.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→10 Å
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Refine LS restraints |
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