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Yorodumi- PDB-5mh4: Crystal Structure of Lactococcus lactis Thioredoxin Reductase (FR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mh4 | ||||||
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Title | Crystal Structure of Lactococcus lactis Thioredoxin Reductase (FR conformation) | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / Thioredoxin Reductase / photosensitivity / Reactive Oxygen Species / FAD si-face open space / Oxygen pocket / FAD-NADP+ complex / FO-FR conformations | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Skjoldager, N. / Bang, M.B. / Svensson, B. / Hagglund, P. / Harris, P. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mh4.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mh4.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/5mh4 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/5mh4 | HTTPS FTP |
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-Related structure data
Related structure data | 5mipC 5miqC 5mirC 5misC 5mitC 5mjkC 1f6mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.1021/bi5013639 / Data set type: other data |
-Links
-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.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Gene: N41_1746, NCDO763_0431 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: A0A166TWQ7, UniProt: A2RLJ5*PLUS, thioredoxin-disulfide reductase |
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-Non-polymers , 5 types, 171 molecules
#2: Chemical | ChemComp-FAD / | ||
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#3: Chemical | ChemComp-NAP / | ||
#4: Chemical | ChemComp-PEG / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.94 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96501 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 16, 2015 / Details: Automatic data collection on ESRF Massif1 ID30A-1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96501 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→85.24 Å / Num. obs: 25158 / % possible obs: 99.9 % / Redundancy: 8.38 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 8.46 % / Rmerge(I) obs: 1.744 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F6M Resolution: 2.14→49.37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.311 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.171 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: 122.63 Å2 / Biso mean: 43.954 Å2 / Biso min: 23.31 Å2
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Refinement step | Cycle: final / Resolution: 2.14→49.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.196 Å / Total num. of bins used: 20
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