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- PDB-5mis: Crystal Structure of Lactococcus lactis Thioredoxin Reductase Exp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mis | ||||||
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Title | Crystal Structure of Lactococcus lactis Thioredoxin Reductase Exposed to Visible Light (180 min) | ||||||
![]() | Thioredoxin reductase | ||||||
![]() | OXIDOREDUCTASE / Thioredoxin Reductase / photosensitivity / Reactive Oxygen Species / FAD si-face open space / Oxygen pocket / FAD-NADP+ complex / FO-FR conformations | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Skjoldager, N. / Bang, M.B. / Svensson, B. / Hagglund, P. / Harris, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage. Authors: Skjoldager, N. / Blanner Bang, M. / Rykr, M. / Bjornberg, O. / Davies, M.J. / Svensson, B. / Harris, P. / Hagglund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 62.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mh4C ![]() 5mipC ![]() 5miqC ![]() 5mirC ![]() 5mitC ![]() 5mjkC ![]() 1f6mS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36026.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: N41_1746, NCDO763_0431 / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: A0A166TWQ7, UniProt: A2RLJ5*PLUS, thioredoxin-disulfide reductase |
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-Non-polymers , 5 types, 260 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-NAP / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.77 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 35% PEG 1500, 400 mM Li2SO4, 20 mM HEPES / PH range: 6.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→85.51 Å / Num. obs: 41622 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.063 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.317 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F6M Resolution: 1.81→54.13 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.73 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.112 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.08 Å2 / Biso mean: 30.017 Å2 / Biso min: 13.11 Å2
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Refinement step | Cycle: final / Resolution: 1.81→54.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.806→1.853 Å / Total num. of bins used: 20
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