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- PDB-1jjg: Solution Structure of Myxoma Virus Protein M156R -

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Basic information

Entry
Database: PDB / ID: 1jjg
TitleSolution Structure of Myxoma Virus Protein M156R
ComponentsM156R
KeywordsVIRAL PROTEIN / beta barrel / S1 motif / OB Fold / MYXV156R / NESG PROJECT / STRUCTURAL GENOMICS / EIF-2a HOMOLOG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyNucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / M156R
Function and homology information
Biological speciesMyxoma virus
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Yee, A.A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Myxoma virus immunomodulatory protein M156R is a structural mimic of eukaryotic translation initiation factor eIF2alpha.
Authors: Ramelot, T.A. / Cort, J.R. / Yee, A.A. / Liu, F. / Goshe, M.B. / Edwards, A.M. / Smith, R.D. / Arrowsmith, C.H. / Dever, T.E. / Kennedy, M.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: An NMR Approach to Structural Proteomics
Authors: Yee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. / Denisov, A. / Lee, C.-H. / Cort, J.R. / Kozlov, G. / ...Authors: Yee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. / Denisov, A. / Lee, C.-H. / Cort, J.R. / Kozlov, G. / Liao, J. / Finak, G. / Chen, L. / Wishart, D. / Lee, W. / McIntosh, L.P. / Kalle Gehring, K. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionJul 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 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: M156R


Theoretical massNumber of molelcules
Total (without water)11,9971
Polymers11,9971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein M156R


Mass: 11997.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus (strain Lausanne) / Genus: Leporipoxvirus / Species: Myxoma virus / Strain: Lausanne / Gene: M156R / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-lamdaDE3 / References: UniProt: Q9Q8E9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1224D 13C/15N-separated NOESY
133HNHA
1442H EXCHANGE
155NH HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM M156R, U-15N, 13C; 25 mM phosphate buffer, pH 6.590% H2O/10% D2O
21 mM M156R, U-15N, 13C; 25 mM phosphate buffer, pH 6.199% D2O, 1% H2O
31 mM M156R, U-15N; 25 mM phosphate buffer, pH 6.590% H2O/10% D2O
Sample conditionsIonic strength: 450 mM NaCl, 25 mM Na2PO4 / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.84Brungerstructure solution
Felix98MSIprocessing
VNMRVariancollection
Sparky3.1Goddard, Knellerdata analysis
X-PLOR3.84Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: 326 NOE-derived restraints, 66 dihedral angle restraints, 48 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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