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- PDB-2mch: Backbone 1H, 13C, and 15N Chemical Shift Assignments for murine n... -

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Basic information

Entry
Database: PDB / ID: 2mch
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for murine norovirus NS1/2 CW3 WT
ComponentsMurine norovirus 1
KeywordsHYDROLASE / Norovirus / NS1/2
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / RNA helicase activity / 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 / 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 speciesMurine norovirus 1
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsBorin, B. / Krezel, A.M.
CitationJournal: Proteins / Year: 2014
Title: Murine norovirus protein NS1/2 aspartate to glutamate mutation, sufficient for persistence, reorients side chain of surface exposed tryptophan within a novel structured domain.
Authors: Borin, B.N. / Tang, W. / Nice, T.J. / McCune, B.T. / Virgin, H.W. / Krezel, A.M.
History
DepositionAug 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Feb 22, 2017Group: Other
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Murine norovirus 1


Theoretical massNumber of molelcules
Total (without water)7,9891
Polymers7,9891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 900structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Murine norovirus 1 /


Mass: 7989.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Strain: CW3 / Gene: NS1/2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80J95

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
122CBCANH
1312D 1H-1H NOESY
1412D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 300 mM sodium chloride, .5 mM entity, DSS, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate, 300 mM sodium chloride, .5 mM [U-100% 13C; U-100% 15N] entity, DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
300 mMsodium chloride-21
.5 mMentity-31
50 mMsodium phosphate-52
300 mMsodium chloride-62
.5 mMentity-7[U-100% 13C; U-100% 15N]2
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ProcheckNMRLaskowski and MacArthurgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 729
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 900 / Conformers submitted total number: 20

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