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Open data
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Basic information
Entry | Database: PDB / ID: 2jgt | ||||||
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Title | Low resolution structure of SPT | ||||||
![]() | SERINE PALMITOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / SPT / PLP / SSPF / SPHINGOLIPID / PYRIDOXAL PHOSPHATE / SERINE PALMITOYL TRANSFERASE | ||||||
Function / homology | ![]() serine C-palmitoyltransferase / sphingolipid metabolic process / biosynthetic process / acyltransferase activity / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yard, B.A. / Carter, L.G. / Johnson, K.A. / Overton, I.M. / Mcmahon, S.A. / Dorward, M. / Liu, H. / Puech, D. / Oke, M. / Barton, G.J. ...Yard, B.A. / Carter, L.G. / Johnson, K.A. / Overton, I.M. / Mcmahon, S.A. / Dorward, M. / Liu, H. / Puech, D. / Oke, M. / Barton, G.J. / Naismith, J.H. / Campopiano, D.J. | ||||||
![]() | ![]() Title: The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis. Authors: Yard, B.A. / Carter, L.G. / Johnson, K.A. / Overton, I.M. / Dorward, M. / Liu, H. / Mcmahon, S.A. / Oke, M. / Puech, D. / Barton, G.J. / Naismith, J.H. / Campopiano, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.1 KB | Display | ![]() |
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PDB format | ![]() | 115.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.8 KB | Display | ![]() |
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Full document | ![]() | 456 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jg2C ![]() 1fc4S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.01732, -0.84203, 0.53915), Vector: |
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Components
#1: Protein | Mass: 45346.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Details: 10% PEG 8K, 0.17 M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 19635 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21 |
Reflection shell | Resolution: 3→3.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FC4 Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.896 / SU B: 43.158 / SU ML: 0.377 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.463 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.86 Å2
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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