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- PDB-6j27: 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: 6j27 | ||||||
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Title | Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine | ||||||
![]() | N(4)-bis(aminopropyl)spermidine synthase | ||||||
![]() | TRANSFERASE / N(4)-bis(aminopropyl)spermidine synthase / POLYAMINE BIOSYNTHESIS / SPERMIDINE / BRANCHED POLYAMINES | ||||||
Function / homology | ![]() N4-bis(aminopropyl)spermidine synthase / polyamine biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / cytoplasm 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 | ![]() | 305.9 KB | Display | ![]() |
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PDB format | ![]() | 244.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 58.7 KB | Display | |
Data in CIF | ![]() | 82.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j26C ![]() 6j28C ![]() 2q3mS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41644.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: bpsA, TT_C0171 / Plasmid: PET28a / Production host: ![]() ![]() References: UniProt: Q72L89, N4-bis(aminopropyl)spermidine synthase |
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-Non-polymers , 6 types, 710 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/N4P.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/N4P.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MTA / #4: Chemical | ChemComp-N4P / #5: Chemical | #6: Chemical | ChemComp-PEG / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Reservoir: 0.04 M sodium chloride , 0.04 M Tris pH 8.0, 27%(v/v) PEG 350MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 156847 / % possible obs: 99.3 % / Redundancy: 5.3 % / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.66→1.71 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Q3M Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.75 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / 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: 28.17 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→50 Å
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Refine LS restraints |
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