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- PDB-5lxj: Solution NMR structure of the X domain of Peste des Petits Rumina... -

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Basic information

Entry
Database: PDB / ID: 5lxj
TitleSolution NMR structure of the X domain of Peste des Petits Ruminants phosphoprotein
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / XD domain Nucleocapsid binding domain / STRUCTURE FROM CYANA 3.97
Function / homology
Function and homology information


viral genome replication / viral nucleocapsid / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPeste-des-petits-ruminants virus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPereira, N. / Piuzzi, M. / Bontems, F. / Eleouet, J.-F. / Sizun, C.
CitationJournal: To Be Published
Title: Solution structure of the X domain of Peste des Petits Ruminants Virus phosphoprotein and interaction with the nucleoprotein
Authors: Pereira, N. / Basbous, N. / Piuzzi, M. / Bontems, F. / Eleouet, J.-F. / Sizun, C.
History
DepositionSep 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)5,9651
Polymers5,9651
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4130 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Phosphoprotein /


Mass: 5964.977 Da / Num. of mol.: 1 / Fragment: X domain, UNP residues 459-509
Source method: isolated from a genetically manipulated source
Details: This peptide contains residues S459-P509. The two N-terminal GS residues are left from an N-terminal GST-tag cleaved with thrombin.
Source: (gene. exp.) Peste-des-petits-ruminants virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91QS4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D HN(COCA)CB
181isotropic13D HN(CO)CA
171isotropic13D HBHA(CO)NH
161isotropic12D NOESY
191isotropic13D 1H-15N NOESY
1121isotropic12D 1H-13C HSQC aliphatic
1112isotropic22D 1H-13C HSQC aliphatic
1102isotropic23D (H)CCH-TOCSY
1132isotropic23D 1H-13C NOESY aliphatic
1142isotropic22D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1200 uM [U-13C; U-15N] PPRV_PXD, 20 mM sodium phosphate, 300 mM sodium chloride, 93% H2O/7% D2O13C15N_H2O93% H2O/7% D2O
solution2200 uM [U-13C; U-15N] PPRV_PXD, 20 mM sodium phosphate, 300 mM sodium chloride, 100% D2O13C15N_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMPPRV_PXD[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
300 mMsodium chloridenatural abundance1
200 uMPPRV_PXD[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
300 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 300 mM / Ionic strength err: 30 / Label: 288K / pH: 7.4 / Pressure: 1 bar / Temperature: 288.0 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.2.2Bruker Biospinprocessing
CcpNmr Analysis2.2.2CCPNchemical shift assignment
TALOS+Yang Shen, NIDDKdata analysis
CcpNmr Analysis2.2.2CCPNpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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