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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
TitleCrystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residues P1 prime - P4 prime of NS7
ComponentsNS6 protease
KeywordsVIRAL PROTEIN / Murine norovirus Protease
Function / homology
Function and homology information


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 / cysteine-type endopeptidase activity ...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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.472 Å
AuthorsLeen, E.N. / Cromwell Jr, H. / Fernandes, H. / Curry, S.
Citation
Journal: Peerj / Year: 2015
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: Journal: PLoS ONE / Year: 2012
Title: Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation.
Authors: Leen, E.N. / Baeza, G. / Curry, S.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS6 protease


Theoretical massNumber of molelcules
Total (without water)18,4391
Polymers18,4391
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.190, 35.360, 52.810
Angle α, β, γ (deg.)90.000, 105.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NS6 protease


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.) Murine norovirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q80J95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ASH

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 286 5.01 %Random selection
Rwork0.2085 5419 --
obs0.2108 5705 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.51 Å2 / Biso mean: 22.82 Å2 / Biso min: 4.99 Å2
Refinement stepCycle: final / Resolution: 2.472→38.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 0 22 1244
Biso mean---28.27 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091251
X-RAY DIFFRACTIONf_angle_d1.0831700
X-RAY DIFFRACTIONf_chiral_restr0.07195
X-RAY DIFFRACTIONf_plane_restr0.005213
X-RAY DIFFRACTIONf_dihedral_angle_d13.774425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4723-3.11470.31661390.24292652279198
3.1147-38.11210.22381470.192627672914100

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