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- PDB-4yv1: Crystal structure of Trypanosoma cruzi spermidine synthase in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yv1 | ||||||
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Title | Crystal structure of Trypanosoma cruzi spermidine synthase in complex with quinolin-8-yl piperidine-1-carboxylate | ||||||
![]() | Spermidine synthase, putative | ||||||
![]() | TRANSFERASE / methyltransferase / polyamine synthesis | ||||||
Function / homology | ![]() spermidine synthase / spermidine synthase activity / polyamine biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amano, Y. / Tateishi, Y. | ||||||
![]() | ![]() Title: Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase Authors: Amano, Y. / Namatame, I. / Tateishi, Y. / Honboh, K. / Tanabe, E. / Niimi, T. / Sakashita, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.2 KB | Display | ![]() |
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PDB format | ![]() | 193.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 47.9 KB | Display | |
Data in CIF | ![]() | 66.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yuvC ![]() 4yuwC ![]() 4yuxC ![]() 4yuyC ![]() 4yuzC ![]() 4yv0C ![]() 4yv2C ![]() 3bwbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34103.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CL Brener / Gene: Tc00.1047053510339.50 / Production host: ![]() ![]() #2: Chemical | ChemComp-S4M / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG4000, ammonium sulfate, bis-Tris / PH range: 5.5 - 6.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→34.15 Å / Num. obs: 92299 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.85→1.898 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.1 / % possible all: 99.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BWB Resolution: 1.85→34.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.476 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.007 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→34.15 Å
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Refine LS restraints |
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