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- PDB-2l90: Solution structure of murine myristoylated msrA -

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Basic information

Entry
Database: PDB / ID: 2l90
TitleSolution structure of murine myristoylated msrA
ComponentsPeptide methionine sulfoxide reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Protein repair / L-methionine-(S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / actin cytoskeleton / cellular response to oxidative stress / midbody / intracellular membrane-bounded organelle / mitochondrion / nucleoplasm ...Protein repair / L-methionine-(S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / actin cytoskeleton / cellular response to oxidative stress / midbody / intracellular membrane-bounded organelle / mitochondrion / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptide Methionine Sulfoxide Reductase; Chain A / Peptide methionine sulphoxide reductase MsrA / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / Mitochondrial peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average, model 1
Model type detailsminimized average
AuthorsGruschus, J.M. / Lim, J. / Piszczek, G. / Levine, R.L. / Tjandra, N.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Characterization and solution structure of mouse myristoylated methionine sulfoxide reductase A.
Authors: Lim, J.C. / Gruschus, J.M. / Ghesquiere, B. / Kim, G. / Piszczek, G. / Tjandra, N. / Levine, R.L.
#1: Journal: J.Biol.Chem. / Year: 2012
Title: A Low pKa cysteine at the active site of mouse methionine sulfoxide reductase A.
Authors: Lim, J.C. / Gruschus, J.M. / Kim, G. / Berlett, B.S. / Tjandra, N. / Levine, R.L.
History
DepositionJan 27, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Aug 1, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9082
Polymers23,6801
Non-polymers2281
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200
RepresentativeModel #1minimized average structure

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Components

#1: Protein Peptide methionine sulfoxide reductase / Peptide-methionine (S)-S-oxide reductase / Peptide Met(O) reductase / Protein-methionine-S-oxide ...Peptide-methionine (S)-S-oxide reductase / Peptide Met(O) reductase / Protein-methionine-S-oxide reductase / PMSR


Mass: 23679.570 Da / Num. of mol.: 1 / Fragment: sequence database residues 22-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msra / Production host: Escherichia coli (E. coli)
References: UniProt: Q9D6Y7, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1212D 1H-15N HSQC
1312D 1H-13C HSQC aliphatic
1413D CBCA(CO)NH
1513D HN(CA)CB

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Sample preparation

DetailsContents: 0.3 mM [U-98% 13C; U-98% 15N] msrA, 5 mM DTT, 50 mM TRIS, 5 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMmsrA-1[U-98% 13C; U-98% 15N]1
5 mMDTT-21
50 mMTRIS-31
5 mMEDTA-41
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The authors state that the distortion around Cys206 CA in model 1 is a manifestation of the averaging, reflecting that local flexibility often cannot be accurately represented as a single structure.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 21

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