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- PDB-5wej: 1.95 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 5wej
Title1.95 A resolution structure of Norovirus 3CL protease in complex with a dipeptidyl oxazolidinone-based inhibitor
ComponentsGenome polyprotein
KeywordsHYDROLASE/HYDROLASE inhibitor / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / Oxazolidinone-based DIPEPTIDYL INHIBITOR / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


calicivirin / host cell membrane / 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 ...calicivirin / host cell membrane / 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 / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-V45 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Damalanka, V.C. / Kim, Y. / Kankanamalage, A.C.G. / Rathnayake, A.D. / Nguyen, H.N. / Chang, K.O. / Groutas, W.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Eur J Med Chem / Year: 2017
Title: Structure-guided design, synthesis and evaluation of oxazolidinone-based inhibitors of norovirus 3CL protease.
Authors: Damalanka, V.C. / Kim, Y. / Galasiti Kankanamalage, A.C. / Rathnayake, A.D. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Nguyen, H.N. / Lushington, G.H. / Chang, K.O. / Groutas, W.C.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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)41,1804
Polymers40,2522
Non-polymers9282
Water2,648147
1
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5902
Polymers20,1261
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5902
Polymers20,1261
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.556, 59.556, 357.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Genome polyprotein


Mass: 20126.131 Da / Num. of mol.: 2 / Fragment: Full length enzyme (UNP residues 1101-1281)
Source method: isolated from a genetically manipulated source
Details: The N-terminal residues (MHHHHHH) are part of the purification tag.
Source: (gene. exp.) Norwalk virus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q83883, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#2: Chemical ChemComp-V45 / (2S)-2-{(5S)-5-[(3-chlorophenyl)methyl]-2-oxo-1,3-oxazolidin-3-yl}-4-methyl-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}pentanamide


Mass: 463.954 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30ClN3O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.27 Å3/Da / Density % sol: 45.9 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% (w/v) PEG 3350, 100 mM bis-Tris, 200 mM lithium suflate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.56 Å / Num. obs: 29026 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 31.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Net I/σ(I): 18.1 / Num. measured all: 542337 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.95-219.61.82519940.7751100
8.94-49.5613.60.0310.999199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.16 Å47.33 Å
Translation6.16 Å47.33 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASER2.7.17phasing
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T6D

5t6d


Resolution: 1.95→36.293 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.46
RfactorNum. reflection% reflection
Rfree0.2287 1400 4.85 %
Rwork0.1879 --
obs0.1899 28871 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.03 Å2 / Biso mean: 35.1632 Å2 / Biso min: 16.86 Å2
Refinement stepCycle: final / Resolution: 1.95→36.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 48 147 2616
Biso mean--37.18 41.49 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012544
X-RAY DIFFRACTIONf_angle_d1.023464
X-RAY DIFFRACTIONf_chiral_restr0.064399
X-RAY DIFFRACTIONf_plane_restr0.007439
X-RAY DIFFRACTIONf_dihedral_angle_d13.7431486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-2.01970.28021460.237426462792
2.0197-2.10060.25641360.20826782814
2.1006-2.19620.21441170.199727042821
2.1962-2.3120.25991280.193826742802
2.312-2.45680.27241360.183927092845
2.4568-2.64640.24761390.195826902829
2.6464-2.91260.24971380.189727282866
2.9126-3.33380.22041380.194527952933
3.3338-4.19930.19661490.16728162965
4.1993-36.29910.22451730.18830313204

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