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- PDB-4x2y: Crystal structure of a chimeric Murine Norovirus NS6 protease (in... -

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Basic information

Entry
Database: PDB / ID: 4x2y
TitleCrystal structure of a chimeric Murine Norovirus NS6 protease (inactive C139A mutant) in which the P4-P4 prime residues of the cleavage junction in the extended C-terminus have been replaced by the corresponding residues from the NS2-3 junction.
ComponentsNS6 Protease,NS6 Protease
KeywordsVIRAL PROTEIN / Murine norovirus / Protease
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
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: 2.417 Å
AuthorsLeen, E.N. / Pfeil, M.-P. / 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,NS6 Protease
B: NS6 Protease,NS6 Protease


Theoretical massNumber of molelcules
Total (without water)37,6492
Polymers37,6492
Non-polymers00
Water1,928107
1
A: NS6 Protease,NS6 Protease


Theoretical massNumber of molelcules
Total (without water)18,8251
Polymers18,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS6 Protease,NS6 Protease


Theoretical massNumber of molelcules
Total (without water)18,8251
Polymers18,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.520, 47.320, 53.070
Angle α, β, γ (deg.)104.450, 91.530, 110.610
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NS6 Protease,NS6 Protease


Mass: 18824.516 Da / Num. of mol.: 2 / Fragment: UNP residues 998-1173,UNP residues 338-340 / Mutation: C139A,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 / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
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 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.417→19.273 Å / Num. obs: 10817 / % possible obs: 91.14 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.7
Reflection shellResolution: 2.417→2.503 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.31 / % possible all: 66.47

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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: 2.417→19.273 Å / FOM work R set: 0.8164 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 538 5 %Random selection
Rwork0.2104 10231 --
obs0.2129 10769 90.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.93 Å2 / Biso mean: 28.3 Å2 / Biso min: 20.56 Å2
Refinement stepCycle: final / Resolution: 2.417→19.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 107 2669
Biso mean---28.25 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032625
X-RAY DIFFRACTIONf_angle_d0.6733572
X-RAY DIFFRACTIONf_chiral_restr0.046408
X-RAY DIFFRACTIONf_plane_restr0.003448
X-RAY DIFFRACTIONf_dihedral_angle_d12.543888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4171-2.65980.31681200.27522269238981
2.6598-3.04330.33861330.25162605273893
3.0433-3.82940.26151410.2072668280994
3.8294-19.27370.20761440.17332689283395

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