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- PDB-3zfn: Crystal structure of product-like, processed N-terminal protease Npro -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zfn | ||||||
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Title | Crystal structure of product-like, processed N-terminal protease Npro | ||||||
![]() | N-TERMINAL PROTEASE NPRO | ||||||
![]() | HYDROLASE / AUTO-PROCESSING CYSTEINE PROTEASE / VIRAL PROTEASE / IN CIS- CLEAVAGE / HYDROXIDE-DEPENDENT CATALYSIS / AUTO-PROTEOLYSIS / IMMUNE MODULATION / HOST-PATHOGEN INTERACTION / CONVERGENT EVOLUTION | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zogg, T. / Sponring, M. / Schindler, S. / Koll, M. / Schneider, R. / Brandstetter, H. / Auer, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.3 KB | Display | ![]() |
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PDB format | ![]() | 60.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
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Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zfoC ![]() 3zfpC ![]() 3zfqC ![]() 3zfrC ![]() 3zftC ![]() 3zfuC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: Q5L4B1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-SGM / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % Description: STRUCTURE WAS SOLVED BY 3W-MAD EXPERIMENT OF A SEMET-EXPRESSED CONSTRUCT. THIS STRUCTURE SERVED AS MR- MODEL TO SOLVE THE NATIVE DATASET. |
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Crystal grow | pH: 8.5 / Details: 100MM NA ACETATE, PH8.5 50% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 21445 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.2 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SEMET-SUBSTITUTED PROTEIN Resolution: 1.5→28.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-150 ARE 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: 17.747 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→28.71 Å
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Refine LS restraints |
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