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- PDB-6bq5: Crystal structure of Medicago truncatula Thermospermine Synthase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bq5 | ||||||
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Title | Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with 5'-methylthioadenosine | ||||||
![]() | Thermospermine synthase ACAULIS protein | ||||||
![]() | TRANSFERASE / polyamine biosynthesis / tetraamine / thermospermine / spermidine / aminopropyl transferase | ||||||
Function / homology | ![]() thermospermine synthase activity / spermidine synthase / spermidine synthase activity / polyamine biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sekula, B. / Dauter, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases. Authors: Sekula, B. / Dauter, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.2 KB | Display | ![]() |
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PDB format | ![]() | 204.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bq2SC ![]() 6bq3C ![]() 6bq4C ![]() 6bq6C ![]() 6bq7C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 37279.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.77 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG3350, 0.1 M Magnesium Chloride, 0.1 M Bis-Tris propane buffer cryo 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.66 Å / Num. obs: 53857 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.049 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8457 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BQ2 Resolution: 1.8→47.66 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.212 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.122 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.003 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→47.66 Å
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Refine LS restraints |
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