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- PDB-2a2p: Solution structure of SelM from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 2a2p
TitleSolution structure of SelM from Mus musculus
ComponentsSelenoprotein M
KeywordsOXIDOREDUCTASE / Selenoprotein / Redox enzyme
Function / homology
Function and homology information


corticosterone secretion / response to selenium ion / hormone metabolic process / adipose tissue development / multicellular organism growth / oxidoreductase activity / endoplasmic reticulum lumen / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Sep15/SelM thioredoxin-like domain, active-site redox motif / Selenoprotein F/M domain / Selenoprotein F/M, thioredoxin-like domain superfamily / Selenoprotein F/M / Sep15/SelM redox domain / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Distance geometry Simulated annealing, Molecular dynamics Torsion angle dynamics
AuthorsFerguson, A.D. / Labunskyy, V.M. / Fomenko, D.E. / Chelliah, Y. / Amezcua, C.A. / Rizo, J. / Gladyshev, V.N. / Deisenhofer, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: NMR Structures of the Selenoproteins Sep15 and SelM Reveal Redox Activity of a New Thioredoxin-like Family.
Authors: Ferguson, A.D. / Labunskyy, V.M. / Fomenko, D.E. / Chelliah, Y. / Amezcua, C.A. / Rizo, J. / Gladyshev, V.N. / Deisenhofer, J.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2014Group: Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE RESIDUE 48 IN THE SWISS-PROT ENTRY IS SE_CYS, FOR SELENOCYSTEINE. IN THIS ENTRY, THE ...SEQUENCE RESIDUE 48 IN THE SWISS-PROT ENTRY IS SE_CYS, FOR SELENOCYSTEINE. IN THIS ENTRY, THE SELENOCYSTEINE (SEC) HAS BEEN MUTATED TO CYS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Selenoprotein M


Theoretical massNumber of molelcules
Total (without water)15,0631
Polymers15,0631
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 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Selenoprotein M / SelM protein


Mass: 15062.986 Da / Num. of mol.: 1 / Mutation: U48C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sepm, Selm / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8VHC3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
1413D 13C-separated NOESY

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Sample preparation

DetailsContents: 1 mM 15N,13C-labeled SelM 50 mM phosphate buffer (pH 6)
Solvent system: 90% H2O and 10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe1Delaglio, F.processing
NMRView5.2.2Johnson, B.A.data analysis
ARIA2Nilges, M.refinement
ARIA2Nilges, M.structure solution
RefinementMethod: Distance geometry Simulated annealing, Molecular dynamics Torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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