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- PDB-6t1q: 3C-like protease from Southampton norovirus. -

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Basic information

Entry
Database: PDB / ID: 6t1q
Title3C-like protease from Southampton norovirus.
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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / 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 / 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
Biological speciesSouthampton virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 5, 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


Theoretical massNumber of molelcules
Total (without water)36,5092
Polymers36,5092
Non-polymers00
Water6,846380
1
A: Genome polyprotein
B: Genome polyprotein

A: Genome polyprotein
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)73,0194
Polymers73,0194
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area5890 Å2
ΔGint-30 kcal/mol
Surface area27760 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-7 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.133, 89.359, 61.581
Angle α, β, γ (deg.)90.000, 96.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21B-299-

HOH

31B-313-

HOH

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Components

#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(DE3) (bacteria)
References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 18122.041 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(DE3) (bacteria)
References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate, 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-F / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.3→41.29 Å / Num. obs: 83130 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 13.6
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6151 / CC1/2: 0.553 / Rpim(I) all: 0.606 / Rrim(I) all: 1.525 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iph

1iph


Resolution: 1.3→41.29 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.289 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.052
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 4216 5.1 %RANDOM
Rwork0.1508 ---
obs0.1534 78439 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.64 Å2 / Biso mean: 25.55 Å2 / Biso min: 8.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.04 Å2
2---0.24 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.3→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 0 380 2896
Biso mean---43.36 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132686
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172577
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.643667
X-RAY DIFFRACTIONr_angle_other_deg1.4071.575962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7445360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18219.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04815440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5531521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02598
X-RAY DIFFRACTIONr_rigid_bond_restr5.20335262
LS refinement shellResolution: 1.3→1.333 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 260 -
Rwork0.395 5642 -
all-5902 -
obs--95.64 %

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