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Yorodumi- PDB-8iyt: Crystal Structure of Serine Palmitoyltransferase complexed with D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iyt | ||||||
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Title | Crystal Structure of Serine Palmitoyltransferase complexed with D-methylserine | ||||||
Components | Serine palmitoyltransferase | ||||||
Keywords | TRANSFERASE / sphingolipid | ||||||
Function / homology | Function and homology information 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 | Sphingobacterium multivorum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Takahashi, A. / Murakami, T. / Katayama, A. / Miyahara, I. / Kamiya, N. / Ikushiro, H. / Yano, T. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iyt.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iyt.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 8iyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iyt_validation.pdf.gz | 836.7 KB | Display | wwPDB validaton report |
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Full document | 8iyt_full_validation.pdf.gz | 838.9 KB | Display | |
Data in XML | 8iyt_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 8iyt_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iyt ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iyt | HTTPS FTP |
-Related structure data
Related structure data | 8iypC 3a2bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Sphingobacterium multivorum (bacteria) / Gene: spt, I6J33_20140, NCTC11343_02561, SPHINGO8BC_150128 / Production host: Escherichia coli (E. coli) / References: UniProt: A7BFV6, serine C-palmitoyltransferase | ||||
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#2: Chemical | ChemComp-S5R / ( Mass: 350.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N2O8P / Feature type: SUBJECT OF INVESTIGATION | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 44526 / % possible obs: 97.5 % / Redundancy: 10.1 % / CC1/2: 0.999 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Num. unique obs: 7144 / CC1/2: 0.999 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A2B Resolution: 1.7→46.185 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.637 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.116 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: 25.467 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→46.185 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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