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Yorodumi- PDB-1fj2: Crystal structure of the human acyl protein thioesterase 1 at 1.5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fj2 | ||||||
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Title | Crystal structure of the human acyl protein thioesterase 1 at 1.5 A resolution | ||||||
Components | PROTEIN (ACYL PROTEIN THIOESTERASE 1) | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE / SERINE HYDROLASE / SAD / ANOMALOUS DIFFRACTION | ||||||
Function / homology | Function and homology information protein depalmitoylation / palmitoyl[protein] hydrolase / negative regulation of Golgi to plasma membrane protein transport / palmitoyl-(protein) hydrolase activity / phospholipase activity / lipase activity / lysophospholipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / fatty acid transport ...protein depalmitoylation / palmitoyl[protein] hydrolase / negative regulation of Golgi to plasma membrane protein transport / palmitoyl-(protein) hydrolase activity / phospholipase activity / lipase activity / lysophospholipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / fatty acid transport / eNOS activation / fatty acid metabolic process / RAS processing / nuclear membrane / cell surface / endoplasmic reticulum / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Devedjiev, Y. / Dauter, Z. / Kuznetsov, S. / Jones, T. / Derewenda, Z. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A. Authors: Devedjiev, Y. / Dauter, Z. / Kuznetsov, S.R. / Jones, T.L. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fj2.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fj2.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/1fj2 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/1fj2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | IN SOLUTION, THERE IS AN EQUILLIBRIUM OF MONOMERIC AND DIMERIC SPECIES OF HUMAN ACYL PROTEIN THIOESTERASE 1. BIOLOGICAL UNIT OF THE ENZYME is STILL UNCERTAIN. |
-Components
#1: Protein | Mass: 24920.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: O75608, alkylglycerophosphoethanolamine phosphodiesterase #2: Chemical | ChemComp-BR / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 28 - 32% OF SATURATED AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, DI-THIO-THREITOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.91374 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Apr 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91374 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. all: 163216 / Num. obs: 50736 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 27 |
Reflection | *PLUS Redundancy: 3.2 % / Num. measured all: 163216 |
Reflection shell | *PLUS % possible obs: 27.1 % / Rmerge(I) obs: 0.343 |
-Processing
Software |
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Refinement | Resolution: 1.5→20 Å / SU B: 2.2 / SU ML: 0.08 / σ(F): 1 / ESU R: 0.11 / ESU R Free: 0.12
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / σ(F): 1 / % reflection Rfree: 2.5 % / Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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