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Yorodumi- PDB-6tr8: Corynebacterium diphtheriae methionine sulfoxide reductase B (Msr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tr8 | ||||||
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Title | Corynebacterium diphtheriae methionine sulfoxide reductase B (MsrB) solution structure - reduced form | ||||||
Components | Peptide-methionine (R)-S-oxide reductase | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing / torsion angle dynamics | ||||||
Authors | Volkov, A.N. / Tossounian, M.A. / Buts, L. / Messens, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tr8.cif.gz | 817.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tr8.ent.gz | 680 KB | Display | PDB format |
PDBx/mmJSON format | 6tr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tr8_validation.pdf.gz | 408 KB | Display | wwPDB validaton report |
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Full document | 6tr8_full_validation.pdf.gz | 538.4 KB | Display | |
Data in XML | 6tr8_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 6tr8_validation.cif.gz | 73.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/6tr8 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/6tr8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 165 mM / Label: MsrB / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement |
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NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |