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Yorodumi- PDB-8pr6: Crystal structure of Corynebacterium glutamicum mycoredoxin-3 at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pr6 | ||||||
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Title | Crystal structure of Corynebacterium glutamicum mycoredoxin-3 at 1.7 A resolution. | ||||||
Components | Thioredoxin family protein | ||||||
Keywords | OXIDOREDUCTASE / Mycoredoxin / Corynebacterium glutamicum / oxidase / swapped homodimer / redox biology | ||||||
Function / homology | Glutaredoxin-like / Glutaredoxin-like domain (DUF836) / Thioredoxin-like superfamily / Thioredoxin family protein Function and homology information | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Baranova, E.V. / Wahni, K. / Ezerina, D. / Messens, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Redox Biochem. Chem. / Year: 2023 Title: Unveiling the enigmatic traits of Corynebacterium glutamicum mycoredoxin-3: A tiny redox protein displaying swapped homodimer formation and DsbA-like oxidase activity Authors: Wahni, K. / Baranova, E. / Ezerina, D. / Van Molle, I. / Van Laer, K. / Messens, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pr6.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pr6.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pr6_validation.pdf.gz | 412.8 KB | Display | wwPDB validaton report |
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Full document | 8pr6_full_validation.pdf.gz | 412.8 KB | Display | |
Data in XML | 8pr6_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 8pr6_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8pr6 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8pr6 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9557.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: AUO95_11055 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q6BKH4 #2: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.2 M MgCl2, 0.1 M Bis-Tris (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9195 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.4 Å / Num. obs: 19317 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.081 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2791 / Rrim(I) all: 0.82 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.279 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.009 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→32.23 Å
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