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- PDB-6tr8: Corynebacterium diphtheriae methionine sulfoxide reductase B (Msr... -

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Basic information

Entry
Database: PDB / ID: 6tr8
TitleCorynebacterium diphtheriae methionine sulfoxide reductase B (MsrB) solution structure - reduced form
ComponentsPeptide-methionine (R)-S-oxide reductase
KeywordsOXIDOREDUCTASE / Methionine sulfoxide reductase / reduced structure / catalytic cysteines / zinc-coordination
Function / homology
Function and homology information


peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / response to oxidative stress
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
Peptide-methionine (R)-S-oxide reductase / Peptide-methionine (R)-S-oxide reductase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsVolkov, A.N. / Tossounian, M.A. / Buts, L. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1508316N Belgium
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Methionine sulfoxide reductase B fromCorynebacterium diphtheriaecatalyzes sulfoxide reduction via an intramolecular disulfide cascade.
Authors: Tossounian, M.A. / Khanh Truong, A.C. / Buts, L. / Wahni, K. / Mourenza, A. / Leermakers, M. / Vertommen, D. / Mateos, L.M. / Volkov, A.N. / Messens, J.
History
DepositionDec 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide-methionine (R)-S-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5372
Polymers17,4711
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8640 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptide-methionine (R)-S-oxide reductase


Mass: 17471.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence contains an N-terminal 6x Histidine-tag
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: msrB, B11Q_01469, B1A51_07985, BT093_04380 / Production host: Escherichia coli (E. coli) / Variant (production host): Rossetta (DE3)
References: UniProt: A0A0D6GDN9, UniProt: Q6NGV7*PLUS, peptide-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HN(COCA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-13C HSQC
1101isotropic12D 1H-13C HSQC aromatic
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic12D (HB)CB(CGCD)HD
1151isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] MsrB, 20 mM sodium phosphate, 150 mM sodium chloride, 2 mM DTT, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O
Label: MsrB / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMsrB[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
10 %D2O[U-100% 2H]1
Sample conditionsIonic strength: 165 mM / Label: MsrB / pH: 7.0 / Pressure: 1 atm / Temperature: 298 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
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
simulated annealing8
torsion angle dynamics9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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