+Open data
-Basic information
Entry | Database: PDB / ID: 7d6l | ||||||
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Title | Crystal structure of Trx2 from D. radiodurans R1 | ||||||
Components | Thioredoxin 2 | ||||||
Keywords | OXIDOREDUCTASE / antioxidant / thioredoxin / redox control / cysteine thiol-disulfide exchange | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.947 Å | ||||||
Authors | Kim, M.-K. / Zhang, J. / Zhao, L. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Antioxidants / Year: 2021 Title: Structural and Biochemical Characterization of Thioredoxin-2 from Deinococcus radiodurans. Authors: Kim, M.-K. / Zhao, L. / Jeong, S. / Zhang, J. / Jung, J.-H. / Seo, H.S. / Choi, J.- / Lim, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d6l.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d6l.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 7d6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d6l_validation.pdf.gz | 976.4 KB | Display | wwPDB validaton report |
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Full document | 7d6l_full_validation.pdf.gz | 977.6 KB | Display | |
Data in XML | 7d6l_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 7d6l_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6l ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6l | HTTPS FTP |
-Related structure data
Related structure data | 1v98S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16383.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Strain: R1 / Gene: DR_A0164 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RYY9 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.02 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: PEG 3350, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.947→50 Å / Num. obs: 14566 / % possible obs: 94.9 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Net I/σ(I): 50.779 |
Reflection shell | Resolution: 1.947→1.99 Å / Mean I/σ(I) obs: 11.628 / Num. unique obs: 685 / CC1/2: 0.971 / Rpim(I) all: 0.118 / Rrim(I) all: 0.262 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1v98 Resolution: 1.947→18.935 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 22.99 / 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: 108.28 Å2 / Biso mean: 38.3938 Å2 / Biso min: 13.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.947→18.935 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 35.221 Å / Origin y: 50.7825 Å / Origin z: 6.1787 Å
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Refinement TLS group |
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