+Open data
-Basic information
Entry | Database: PDB / ID: 6dft | ||||||
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Title | Trypanosoma brucei deoxyhypusine synthase | ||||||
Components |
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Keywords | TRANSFERASE / heterotetramer / Rossman fold / pseudoenzyme / NAD+ | ||||||
Function / homology | Function and homology information : / biological process involved in symbiotic interaction / deoxyhypusine synthase / deoxyhypusine synthase activity / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / protein heterotetramerization / positive regulation of catalytic activity / catalytic complex / enzyme activator activity ...: / biological process involved in symbiotic interaction / deoxyhypusine synthase / deoxyhypusine synthase activity / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / protein heterotetramerization / positive regulation of catalytic activity / catalytic complex / enzyme activator activity / : / membrane => GO:0016020 / positive regulation of gene expression / enzyme binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Model details | Active enzyme is a heterotetramer, composed of a heterodimer of the catalytic and pseudoenzyme monomers. | ||||||
Authors | Tomchick, D.R. / Phillips, M.A. / Afanador, G.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2018 Title: Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation between Pseudoenzyme Paralogs. Authors: Afanador, G.A. / Tomchick, D.R. / Phillips, M.A. #1: Journal: J Biol Chem / Year: 2013 Title: Allosteric Activation of Trypanosomatid Deoxyhypusine Synthase by a Catalytically Dead Paralog Authors: Suong, N. / Jones, D.C. / Wyllie, S. / Fairlamb, A.H. / Phillips, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dft.cif.gz | 786.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dft.ent.gz | 653.9 KB | Display | PDB format |
PDBx/mmJSON format | 6dft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dft ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dft | HTTPS FTP |
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-Related structure data
Related structure data | 1rqdS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 50226.137 Da / Num. of mol.: 6 / Fragment: catalytic monomer Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: DHSc / Plasmid: pETDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38BX0, deoxyhypusine synthase #2: Protein | Mass: 37419.312 Da / Num. of mol.: 6 / Fragment: pseudoenzyme monomer Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: DHSp / Plasmid: pETDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4GZD1, deoxyhypusine synthase #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-NAD / |
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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: 1.98 Å3/Da / Density % sol: 37.66 % / Description: THIN PLATE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES, 10 mM TCEP, 2 mM NAD+, 8% PEG 6000, 20% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2017 / Details: monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→50 Å / Num. obs: 52848 / % possible obs: 97.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 64.48 Å2 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.101 / Rrim(I) all: 0.214 / Χ2: 0.87 / Net I/σ(I): 4.1 / Num. measured all: 214291 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RQD Resolution: 3.5→48.752 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.42 Å2 / Biso mean: 57.1506 Å2 / Biso min: 23.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→48.752 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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