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Open data
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Basic information
Entry | Database: PDB / ID: 6tor | ||||||
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Title | human O-phosphoethanolamine phospho-lyase | ||||||
![]() | Ethanolamine-phosphate phospho-lyase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vettraino, C. / Donini, S. / Parisini, E. | ||||||
![]() | ![]() Title: Structural characterization of human O-phosphoethanolamine phospho-lyase. Authors: Vettraino, C. / Peracchi, A. / Donini, S. / Parisini, E. #1: ![]() Title: Structural characterization of human O-phosphoethanolamine phospho-lyase. Authors: Vettraino, C. / Peracchi, S. / Donini, S. / Parisini, 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 | ![]() | 184.1 KB | Display | ![]() |
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PDB format | ![]() | 143.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5g4iS S: Starting model for refinement |
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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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Components
#1: Protein | ![]() Mass: 55757.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8TBG4, ![]() #2: Chemical | ChemComp-GOL / ![]() #3: Chemical | #4: 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: 1.93 Å3/Da / Density % sol: 36.15 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 100 mM Bis Tris propane pH 7.0, 200 mM ammonium sulfate, and 3% MPD. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→69.09 Å / Num. obs: 54318 / % possible obs: 99.99 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.068 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.05→2.16 Å / Rmerge(I) obs: 0.102 / Num. unique obs: 54318 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5G4I Resolution: 2.05→69.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.186 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.21 Å2 / Biso mean: 21 Å2 / Biso min: 4.75 Å2
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Refinement step | Cycle: final / Resolution: 2.05→69.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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