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- PDB-1fxw: CRYSTAL STRUCTURE OF THE RECOMBINANT ALPHA1/ALPHA2 CATALYTIC HETE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fxw | ||||||
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Title | CRYSTAL STRUCTURE OF THE RECOMBINANT ALPHA1/ALPHA2 CATALYTIC HETERODIMER OF BOVINE BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB. | ||||||
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![]() | HYDROLASE / alpha beta hydrolase fold | ||||||
Function / homology | ![]() platelet-activating factor acetyltransferase activity / 1-alkyl-2-acetylglycerophosphocholine esterase complex / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Neutrophil degranulation / positive regulation of macroautophagy / lipid catabolic process / brain development / fibrillar center ...platelet-activating factor acetyltransferase activity / 1-alkyl-2-acetylglycerophosphocholine esterase complex / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Neutrophil degranulation / positive regulation of macroautophagy / lipid catabolic process / brain development / fibrillar center / spermatogenesis / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Derewenda, Z. / Li, J. | ||||||
![]() | ![]() Title: Preparation and crystal structure of the recombinant alpha(1)/alpha(2) catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib. Authors: Sheffield, P.J. / McMullen, T.W. / Li, J. / Ho, Y.S. / Garrard, S.M. / Derewenda, U. / Derewenda, Z.S. #1: ![]() Title: Brain Acetylhydrolase that Inactivates Platelet-activating Factor is a G-protein-like Trimer Authors: Ho, Y.S. / Swenson, L. / Derewenda, U. / Serre, L. / Wei, Y. / Dauter, Z. / Hattori, M. / Adachi, T. / Aoki, J. / Arai, H. / Inoue, K. / Derewenda, Z.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.4 KB | Display | ![]() |
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Full document | ![]() | 432.5 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is alpha1/alpha1 homodimer, alpha1/alpha2 heterodimer and alpha2/alpha2 homodimer |
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Components
#1: Protein | Mass: 25903.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase |
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#2: Protein | Mass: 25600.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P68401, 1-alkyl-2-acetylglycerophosphocholine esterase |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 17% PEG-MME 2000, 100 mM Na acetate, pH 6.4, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0084 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→20 Å / Num. all: 26093 / Num. obs: 25752 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.83 % / Biso Wilson estimate: 30.98 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.63 |
Reflection shell | Resolution: 2.07→20 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.371 / Num. unique all: 2848 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. obs: 25073 / % possible obs: 99.1 % / Num. measured all: 273571 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.335 |
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Processing
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Refinement | Resolution: 2.1→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: residues A53 to A63 were not included in the final refinement
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 1 / Rfactor obs: 0.218 / Rfactor Rfree: 0.277 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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