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Yorodumi- PDB-5y4p: Crystal structure of Trypanosoma cruzi spermidine synthase in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y4p | ||||||
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Title | Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 5-methoxy-2-(5-methyl-4,5-dihydro-1H-imidazol-2-yl)phenol | ||||||
Components | Spermidine synthase, putative | ||||||
Keywords | TRANSFERASE / polyamine synthesis | ||||||
Function / homology | Function and homology information spermidine synthase / spermidine synthase activity / polyamine biosynthetic process Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Amano, Y. / Tateishi, Y. | ||||||
Citation | Journal: Acs Omega / Year: 2023 Title: Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro , and X-ray Crystallography. Authors: Yoshino, R. / Yasuo, N. / Hagiwara, Y. / Ishida, T. / Inaoka, D.K. / Amano, Y. / Tateishi, Y. / Ohno, K. / Namatame, I. / Niimi, T. / Orita, M. / Kita, K. / Akiyama, Y. / Sekijima, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y4p.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y4p.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 5y4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/5y4p ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y4p | HTTPS FTP |
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-Related structure data
Related structure data | 5y4qC 5b1sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053510339.50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DA73, spermidine synthase #2: Chemical | ChemComp-S4M / #3: Chemical | ChemComp-8QO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris, Ammonium sulfate, PEG4000 / PH range: 5.5 - 6.0 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 60679 / % possible obs: 94.2 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.7 / % possible all: 93.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B1S Resolution: 2.16→49.86 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.65 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.246 / 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: 40.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→49.86 Å
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Refine LS restraints |
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