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- PDB-1jq3: Crystal Structure of Spermidine Synthase in Complex with Transiti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jq3 | ||||||
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Title | Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO | ||||||
![]() | Spermidine synthase | ||||||
![]() | TRANSFERASE / aminopropyltransferase / homo-tetramer / thermophyle / transition-state analogue / beta-barrel / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() sym-norspermidine synthase activity / agmatine aminopropyltransferase activity / cadaverine aminopropyltransferase activity / thermospermine synthase activity / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Korolev, S. / Ikeguchi, Y. / Skarina, T. / Beasley, S. / Edwards, A. / Joachimiak, A. / Pegg, A.E. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Authors: Korolev, S. / Ikeguchi, Y. / Skarina, T. / Beasley, S. / Arrowsmith, C. / Edwards, A. / Joachimiak, A. / Pegg, A.E. / Savchenko, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.8 KB | Display | ![]() |
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PDB format | ![]() | 208.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 51.7 KB | Display | |
Data in CIF | ![]() | 72.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1inlSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34184.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.42 % | ||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 4.4 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-1 / Detector: CCD / Date: May 24, 2001 |
Radiation | Monochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 138175 / Num. obs: 126154 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2 / % possible all: 72.5 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 72.5 % / Rmerge(I) obs: 0.556 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1INL Resolution: 1.8→46.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2808531.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.4057 Å2 / ksol: 0.335983 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→46.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection obs: 112302 / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.251 |