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Yorodumi- PDB-7e43: Structural insights into a bifunctional peptide methionine sulfox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+43 | ||||||
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Title | Structural insights into a bifunctional peptide methionine sulfoxide reductase MsrA/B fusion protein from Helicobacter pylori | ||||||
Components | Peptide methionine sulfoxide reductase MsrA/MsrB | ||||||
Keywords | OXIDOREDUCTASE / MsrAB / fusion protein / linker region | ||||||
Function / homology | Function and homology information L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein modification process => GO:0036211 / response to oxidative stress / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori 26695 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kim, S. / Lee, K. / Hwang, K.Y. | ||||||
Citation | Journal: Antioxidants (Basel) / Year: 2021 Title: Structural Insights into a Bifunctional Peptide Methionine Sulfoxide Reductase MsrA/B Fusion Protein from Helicobacter pylori . Authors: Kim, S. / Lee, K. / Park, S.H. / Kwak, G.H. / Kim, M.S. / Kim, H.Y. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e43.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e43.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 7e43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e43_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7e43_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7e43_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 7e43_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/7e43 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/7e43 | HTTPS FTP |
-Related structure data
Related structure data | 3e0mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41309.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: msrAB, msrA, HP_0224 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 References: UniProt: O25011, peptide-methionine (S)-S-oxide reductase, peptide-methionine (R)-S-oxide reductase #2: Chemical | ChemComp-ACT / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate pH 4.6 and 2.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. obs: 53424 / % possible obs: 94.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Χ2: 2.566 / Net I/σ(I): 16.4 / Num. measured all: 163323 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E0M Resolution: 2.2→27.59 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.26 / Phase error: 22.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.95 Å2 / Biso mean: 39.0177 Å2 / Biso min: 12.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→27.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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