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Open data
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Basic information
Entry | Database: PDB / ID: 1ei9 | |||||||||
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Title | CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 | |||||||||
![]() | PALMITOYL PROTEIN THIOESTERASE 1 | |||||||||
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Function / homology | ![]() long-chain fatty acyl-CoA hydrolase activity / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bellizzi III, J.J. / Widom, J. / Kemp, C. / Lu, J.Y. / Das, A.K. / Hofmann, S.L. / Clardy, J. | |||||||||
![]() | ![]() Title: The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis. Authors: Bellizzi III, J.J. / Widom, J. / Kemp, C. / Lu, J.Y. / Das, A.K. / Hofmann, S.L. / Clardy, J. #1: ![]() Title: Producing Selenomethionine-labeled Proteins with a Baculovirus Expression Vector System Authors: Bellizzi III, J.J. / Widom, J. / Kemp, C.W. / Clardy, J. #2: ![]() Title: Mutations in the Palmitoyl Protein Thioesterase Gene Causing Infantile Neuronal Ceroid Lipofuscinosis Authors: Vesa, J. / Hellsten, E. / Verkruyse, L.A. / Camp, L.A. / Rapola, J. / Santavuori, P. / Hofmann, S.L. / Peltonen, L. #3: ![]() Title: Purification and Properties of a Palmitoyl-Protein Thioesterase That Cleaves Palmitate from H-Ras Authors: Camp, L.A. / Hofmann, S.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.8 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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
#1: Protein | Mass: 31447.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||
#3: Sugar | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 55% Polypropylene Glycol 400, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.25→20.33 Å / Num. all: 15553 / Num. obs: 14962 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4 % / Rmerge(I) obs: 0.125 / % possible all: 92.4 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 20.9 Å / Num. obs: 14788 / % possible obs: 94.8 % / Num. measured all: 109210 / Rmerge(I) obs: 0.055 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 91.4 % / Rmerge(I) obs: 0.164 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: anisotropic B correction and bulk solvent correction applied. Maximum likelihood target function used. The structure was determined by MAD phasing at 3.0 Angstroms on SeMet protein expressed ...Details: anisotropic B correction and bulk solvent correction applied. Maximum likelihood target function used. The structure was determined by MAD phasing at 3.0 Angstroms on SeMet protein expressed in baculovirus/insect cells. The model was refined against a 2.25 Angstrom native data set.
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Solvent computation | Solvent model: flat model / Bsol: 75.8949 Å2 / ksol: 0.453878 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.8 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.36 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.284 |