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- PDB-6t5d: 3C-like protease from Southampton virus complexed with FMOPL000014a. -

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Basic information

Entry
Database: PDB / ID: 6t5d
Title3C-like protease from Southampton virus complexed with FMOPL000014a.
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
2-phenylmethoxyaniline / Genome polyprotein
Similarity search - Component
Biological speciesSouthampton virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.42 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 16, 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)36,9743
Polymers36,7752
Non-polymers1991
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Structure suggests tetramer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.800, 89.260, 61.490
Angle α, β, γ (deg.)90.000, 96.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

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-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
#3: Chemical ChemComp-MJW / 2-phenylmethoxyaniline


Mass: 199.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.15 %
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: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.42→61.07 Å / Num. obs: 60967 / % possible obs: 96.4 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 15 / Num. measured all: 179818
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.42-1.462.10.672842840320.5020.6050.9081.286.8
6.35-61.073.20.0222977110.9990.0130.02449.796.2

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6t1q

6t1q


Resolution: 1.42→61.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.905 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ANISOTROPIC U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 3026 5 %RANDOM
Rwork0.1312 ---
obs0.1343 57938 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.8 Å2 / Biso mean: 26.087 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.24 Å2
2---0.31 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.42→61.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 15 395 2987
Biso mean--26.47 45.24 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132738
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172621
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.6423736
X-RAY DIFFRACTIONr_angle_other_deg1.4381.576064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4955368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.90619.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2415445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3151521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_rigid_bond_restr4.71835357
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 226 -
Rwork0.3 3803 -
all-4029 -
obs--86.57 %

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