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- PDB-6j26: Crystal structure of the branched-chain polyamine synthase from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j26 | ||||||
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Title | Crystal structure of the branched-chain polyamine synthase from Thermococcus kodakarensis (Tk-BpsA) in complex with N4-bis(aminopropyl)spermidine and 5'-methylthioadenosine | ||||||
![]() | N(4)-bis(aminopropyl)spermidine synthase | ||||||
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Function / homology | ![]() N4-bis(aminopropyl)spermidine synthase / polyamine biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mizohata, E. / Toyoda, M. / Fujita, J. / Inoue, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis. Authors: Hidese, R. / Toyoda, M. / Yoshino, K.I. / Fukuda, W. / Wihardja, G.A. / Kimura, S. / Fujita, J. / Niitsu, M. / Oshima, T. / Imanaka, T. / Mizohata, E. / Fujiwara, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.9 KB | Display | ![]() |
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PDB format | ![]() | 124.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6j27C ![]() 6j28C ![]() 5xncS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 42445.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: bpsA, TK1691 / Plasmid: PET28a / Production host: ![]() ![]() ![]() References: UniProt: Q5JIZ3, N4-bis(aminopropyl)spermidine synthase #2: Chemical | ![]() #3: Chemical | #4: Chemical | ChemComp-FE / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.93 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Reservoir: 0.015 M tricine pH 8.5, 24%(v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. obs: 44104 / % possible obs: 100 % / Redundancy: 10.1 % / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2→2.07 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5XNC Resolution: 2→40.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.506 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.088 Å2
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Refinement step | Cycle: 1 / Resolution: 2→40.87 Å
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Refine LS restraints |
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