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- PDB-7xii: Crystal structure of the aminopropyltransferase, SpeE from hypert... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xii | ||||||||||||
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Title | Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) & aminopropylagmatine | ||||||||||||
![]() | Polyamine aminopropyltransferase | ||||||||||||
![]() | TRANSFERASE / POLYAMINE BIOSYNTHESIS | ||||||||||||
Function / homology | ![]() thermospermine synthase activity / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mizohata, E. / Yasuda, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis. Authors: Fukuda, W. / Osaki, M. / Yasuda, Y. / Hidese, R. / Higuchi, T. / Umezawa, N. / Fujiwara, S. / Mizohata, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.6 KB | Display | ![]() |
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PDB format | ![]() | 199 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 50.8 KB | Display | |
Data in CIF | ![]() | 70 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xifSC ![]() 7xigC ![]() 7xihC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 34859.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MTA / #3: Chemical | ChemComp-AG3 / #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium formate, HEPES, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.47 Å / Num. obs: 53669 / % possible obs: 99.5 % / Redundancy: 9.9 % / CC1/2: 0.995 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.25→2.32 Å / Num. unique obs: 4661 / CC1/2: 0.961 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7XIF Resolution: 2.25→46.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.416 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.403 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→46.51 Å
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Refine LS restraints |
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