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Yorodumi- PDB-4yux: Crystal structure of Trypanosoma cruzi spermidine synthase in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yux | ||||||
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Title | Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2H-1,4-benzothiazin-3-amine | ||||||
Components | Spermidine synthase, putative | ||||||
Keywords | TRANSFERASE / methyltransferase / 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: 1.6 Å | ||||||
Authors | Amano, Y. / Tateishi, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yux.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yux.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 4yux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yux_validation.pdf.gz | 904.5 KB | Display | wwPDB validaton report |
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Full document | 4yux_full_validation.pdf.gz | 928.6 KB | Display | |
Data in XML | 4yux_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4yux_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/4yux ftp://data.pdbj.org/pub/pdb/validation_reports/yu/4yux | HTTPS FTP |
-Related structure data
Related structure data | 4yuvC 4yuwC 4yuyC 4yuzC 4yv0C 4yv1C 4yv2C 3bwbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34103.723 Da / Num. of mol.: 2 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→24.84 Å / Num. obs: 62982 / % possible obs: 91.05 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.6→1.641 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 4 / % possible all: 95.81 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BWB Resolution: 1.6→23.82 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.467 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.103 / 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: 18.969 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23.82 Å
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Refine LS restraints |
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