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- PDB-2l1u: Structure-Functional Analysis of Mammalian MsrB2 protein -

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Basic information

Entry
Database: PDB / ID: 2l1u
TitleStructure-Functional Analysis of Mammalian MsrB2 protein
ComponentsMethionine-R-sulfoxide reductase B2, mitochondrial
KeywordsOXIDOREDUCTASE / MsrB / Methionine Sulfoxide reductase
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 / response to oxidative stress / mitochondrion ...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 / response to oxidative stress / mitochondrion / zinc ion binding / cytoplasm
Similarity search - Function
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Mss4-like superfamily
Similarity search - Domain/homology
Methionine-R-sulfoxide reductase B2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsfewest violations, model 1
AuthorsAachmann, F.L. / Del Conte, R. / Kwak, G. / Kim, H. / Gladyshev, V.N. / Dikiy, A.
CitationJournal: To be Published
Title: Structure-Functional Analysis of Mammalian MsrB2 protein
Authors: Aachmann, F.L. / Del Conte, R. / Kwak, G. / Kim, H. / Gladyshev, V.N. / Dikiy, A.
History
DepositionAug 6, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine-R-sulfoxide reductase B2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0962
Polymers16,0301
Non-polymers651
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 / 96target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Methionine-R-sulfoxide reductase B2, mitochondrial / MsrB2


Mass: 16030.203 Da / Num. of mol.: 1 / Fragment: residues 45-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msrb2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q78J03, 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 / Details: Structure of den Mouse MsrB2ds
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1233D 1H-15N NOESY
1313D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.6 mM [U-98% 13C; U-98% 15N] MsrB2ds, 5 mM DTT, 20 mM sodium phosphate, 25 mM sodium chloride, 100% D2O100% D2O
21-1.6 mM MsrB2ds, 5 mM DTT, 20 mM sodium phosphate, 25 mM sodium chloride, 100% D2O100% D2O
31-1.6 mM [U-98% 13C; U-98% 15N] MsrB2ds, 5 mM DTT, 20 mM sodium phosphate, 25 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMsrB2ds-1[U-98% 13C; U-98% 15N]1-1.61
5 mMDTT-21
20 mMsodium phosphate-31
25 mMsodium chloride-41
mMMsrB2ds-51-1.62
5 mMDTT-62
20 mMsodium phosphate-72
25 mMsodium chloride-82
mMMsrB2ds-9[U-98% 13C; U-98% 15N]1-1.63
5 mMDTT-103
20 mMsodium phosphate-113
25 mMsodium chloride-123
Sample conditionsIonic strength: 0.1 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameVersionDeveloperClassification
TALOSCornilescu, Delaglio and Baxgeometry optimization
AMBER10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
xwinnmrBruker Biospincollection
XEASYBartels et al.collection
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 96 / Conformers submitted total number: 20

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