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- PDB-6t6w: 3C-like protease from Southampton virus complexed with XST00000692b. -

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Basic information

Entry
Database: PDB / ID: 6t6w
Title3C-like protease from Southampton virus complexed with XST00000692b.
Components(Genome polyprotein) x 2
KeywordsHYDROLASE / Viral protease.
Function / homology
Function and homology information


calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / 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 / ATP binding / membrane / 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 / RNA-directed RNA polymerase, C-terminal domain ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-JL7 / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesSouthampton virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsGuo, J. / Cooper, J.B.
CitationJournal: J Struct Biol X / Year: 2020
Title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors.
Authors: Guo, J. / Douangamath, A. / Song, W. / Coker, A.R. / Chan, A.W.E. / Wood, S.P. / Cooper, J.B. / Resnick, E. / London, N. / Delft, F.V.
History
DepositionOct 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3777
Polymers36,7752
Non-polymers6035
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Structure suggests tetrameric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.940, 89.460, 61.200
Angle α, β, γ (deg.)90.000, 96.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-527-

HOH

21B-545-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Genome polyprotein


Mass: 18387.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Southampton virus (serotype 3) / Gene: ORF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 18387.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Southampton virus (serotype 3) / Gene: ORF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase

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Non-polymers , 4 types, 319 molecules

#3: Chemical ChemComp-JL7 / 2-[4-(trifluoromethyl)phenyl]-1,3-thiazole-4-carboxylic acid


Mass: 273.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H6F3NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: Protein concentration 4 mg/ml. 0.2 M ammonium citrate and 12% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.8→44.73 Å / Num. obs: 30724 / % possible obs: 98.6 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.063 / Rrim(I) all: 0.117 / Net I/σ(I): 8.9 / Num. measured all: 102005
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.850.6681.822630.6470.4240.79399.4
8.05-44.730.04128.83470.9890.0260.04994

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6t1q

6t1q


Resolution: 1.8→44.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.07 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2682 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ANISOTROPIC U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1496 4.9 %RANDOM
Rwork0.144 ---
obs0.149 29227 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.97 Å2 / Biso mean: 25.94 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.22 Å2
2--0.12 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 1.8→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 35 314 2896
Biso mean--54.54 44.33 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172550
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6423645
X-RAY DIFFRACTIONr_angle_other_deg1.3361.5695887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.825346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35219.73111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48815427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.241519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022996
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02585
X-RAY DIFFRACTIONr_rigid_bond_restr2.7335229
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 99 -
Rwork0.261 2159 -
all-2258 -
obs--99.43 %

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