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- PDB-2kv1: Insights into Function, Catalytic Mechanism and Fold Evolution of... -

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Basic information

Entry
Database: PDB / ID: 2kv1
TitleInsights into Function, Catalytic Mechanism and Fold Evolution of Mouse Selenoprotein Methionine Sulfoxide Reductase B1 through Structural Analysis
ComponentsMethionine-R-sulfoxide reductase B1
KeywordsOXIDOREDUCTASE / MsrB1 / SelR / Metal-binding / Nucleus / Selenium
Function / homology
Function and homology information


: / Protein repair / L-methionine (R)-S-oxide reductase / L-methionine-(R)-S-oxide reductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / actin filament polymerization / actin binding / cytoskeleton ...: / Protein repair / L-methionine (R)-S-oxide reductase / L-methionine-(R)-S-oxide reductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / actin filament polymerization / actin binding / cytoskeleton / innate immune response / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulfoxide reductase. / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Methionine-R-sulfoxide reductase B1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsAachmann, F.L. / Sal, L.S. / Kim, H.Y. / Gladyshev, V.N. / Dikiy, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Insights into function, catalytic mechanism, and fold evolution of selenoprotein methionine sulfoxide reductase B1 through structural analysis
Authors: Aachmann, F.L. / Sal, L.S. / Kim, H.Y. / Marino, S.M. / Gladyshev, V.N. / Dikiy, A.
History
DepositionMar 4, 2010Deposition site: BMRB / Processing site: PDBJ
SupersessionMar 16, 2010ID: 2KAO
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Database references
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine-R-sulfoxide reductase B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8972
Polymers13,8321
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 96target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Methionine-R-sulfoxide reductase B1 / MsrB1 / Selenoprotein X / SelX / Selenoprotein R / SelR


Mass: 13831.554 Da / Num. of mol.: 1 / Mutation: SEC95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): ER 2566
References: UniProt: Q9JLC3, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.5mM [U-98% 13C; U-98% 15N] MsrB1-1, 10mM sodium chloride-2, 20mM sodium phosphate-3, 5mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
21-1.5mM [U-98% 13C; U-98% 15N] MsrB1-5, 10mM sodium chloride-6, 20mM sodium phosphate-7, 5mM DTT-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMsrB1-1[U-98% 13C; U-98% 15N]1-1.51
10 mMsodium chloride-21
20 mMsodium phosphate-31
5 mMDTT-41
mMMsrB1-5[U-98% 13C; U-98% 15N]1-1.52
10 mMsodium chloride-62
20 mMsodium phosphate-72
5 mMDTT-82
Sample conditionsIonic strength: 0.06 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance6002

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Processing

NMR software
NameVersionDeveloperClassification
xwinnmr3.5Bruker Biospincollection
xwinnmr3.5Bruker Biospinprocessing
XEASYBartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AMBER10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 96 / Conformers submitted total number: 20 / Representative conformer: 1

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