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- PDB-4x2x: Crystal structure of the Murine Norovirus NS6 protease (inactive ... -
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Basic information
Entry | Database: PDB / ID: 4x2x | ||||||
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Title | Crystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residues P1 prime - P4 prime of NS7 | ||||||
![]() | NS6 protease | ||||||
![]() | VIRAL PROTEIN / Murine norovirus Protease | ||||||
Function / homology | ![]() calicivirin / host cell mitochondrion / ribonucleoside triphosphate phosphatase activity / host cell endosome membrane / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication ...calicivirin / host cell mitochondrion / ribonucleoside triphosphate phosphatase activity / host cell endosome membrane / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Leen, E.N. / Cromwell Jr, H. / Fernandes, H. / Curry, S. | ||||||
![]() | ![]() Title: Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions. Authors: Fernandes, H. / Leen, E.N. / Cromwell, H. / Pfeil, M.P. / Curry, S. #1: ![]() Title: Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation. Authors: Leen, E.N. / Baeza, G. / Curry, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 44.1 KB | Display | ![]() |
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PDB format | ![]() | 30.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4x2vC ![]() 4x2wC ![]() 4x2yC ![]() 4ashS S: Starting model for refinement 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: 18439.098 Da / Num. of mol.: 1 / Fragment: UNP residues 998-1173 / Mutation: C139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M KSCN, 0.1 M Bis-Tris propane pH 6.5-7.5, 20% w/v PEG 3350, cryo 30% (v/v) PEG 3350 PH range: 6.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.472→38.11 Å / Num. obs: 5711 / % possible obs: 99.03 % / Redundancy: 3 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.63 |
Reflection shell | Resolution: 2.472→38.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.94 / % possible all: 92.44 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ASH Resolution: 2.472→38.108 Å / FOM work R set: 0.7988 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 64.51 Å2 / Biso mean: 22.82 Å2 / Biso min: 4.99 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.472→38.108 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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