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- PDB-8iyp: Crystal structure of serine palmitoyltransferase soaked in 190 mM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iyp | ||||||
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Title | Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution | ||||||
![]() | Serine palmitoyltransferase | ||||||
![]() | TRANSFERASE / sphingolipid | ||||||
Function / homology | ![]() 8-amino-7-oxononanoate synthase activity / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / sphingosine biosynthetic process / ceramide biosynthetic process / pyridoxal phosphate binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takahashi, A. / Murakami, T. / Katayama, A. / Miyahara, I. / Kamiya, N. / Ikushiro, H. / Yano, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of Serine Palmitoyltransferase from Sphingobacterium multivorum Authors: Murakami, T. / Takahashi, A. / Kayatama, A. / Miyahara, I. / Kamiya, N. / Ikushiro, H. / Yano, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.6 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iytC ![]() 3a2bS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43822.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PLS / [ | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, sodium acetate, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 47801 / % possible obs: 99.2 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.65→1.75 Å / Num. unique obs: 67830 / CC1/2: 0.991 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A2B Resolution: 1.651→42.248 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.152 / SU B: 1.565 / SU ML: 0.054 / Average fsc free: 0.9763 / Average fsc work: 0.9852 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.093 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.502 Å2
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Refinement step | Cycle: LAST / Resolution: 1.651→42.248 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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