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Yorodumi- PDB-3zfu: Crystal structure of substrate-like, unprocessed N-terminal prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zfu | ||||||
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Title | Crystal structure of substrate-like, unprocessed N-terminal protease Npro mutant S169P with sulphate | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 | 3zfu.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zfu.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zfu_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 3zfu_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 3zfu_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 3zfu_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/3zfu ftp://data.pdbj.org/pub/pdb/validation_reports/zf/3zfu | HTTPS FTP |
-Related structure data
Related structure data | 3zfnSC 3zfoC 3zfpC 3zfqC 3zfrC 3zftC 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: 18396.094 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-SO4 / |
#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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 100MM NAACETATE, PH 8.5 25% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Date: Jul 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→45.46 Å / Num. obs: 14102 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.76→1.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZFN Resolution: 1.76→30.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-150 LARGELY DISORDERED, RESIDUES 171-184 ARE NOT VISIBLE IN THE DENSITY AND ARE NOT INCLUDED IN THE MODEL.
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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: 28.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→30.5 Å
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Refine LS restraints |
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