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Yorodumi- PDB-1es9: X-RAY CRYSTAL STRUCTURE OF R22K MUTANT OF THE MAMMALIAN BRAIN PLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1es9 | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF R22K MUTANT OF THE MAMMALIAN BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES (PAF-AH) | ||||||
Components | PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB GAMMA SUBUNIT | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold | ||||||
Function / homology | Function and homology information 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 / lipid catabolic process / spermatogenesis / protein heterodimerization activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å | ||||||
Authors | McMullen, T.W.P. / Li, J. / Sheffield, P.J. / Aoki, J. / Martin, T.W. / Arai, H. / Inoue, K. / Derewenda, Z.S. | ||||||
Citation | Journal: Protein Eng. / Year: 2000 Title: The functional implications of the dimerization of the catalytic subunits of the mammalian brain platelet-activating factor acetylhydrolase (Ib). Authors: McMullen, T.W. / Li, J. / Sheffield, P.J. / Aoki, J. / Martin, T.W. / Arai, H. / Inoue, K. / Derewenda, Z.S. #1: Journal: Nature / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1es9.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1es9.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 1es9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1es9 ftp://data.pdbj.org/pub/pdb/validation_reports/es/1es9 | 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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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 25875.350 Da / Num. of mol.: 1 / Mutation: R22K / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BRAIN References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.6M Ammonium sulphate, 100mM sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Ho, Y.S., (1999) Protein Eng., 12, 693. | ||||||||||||||||||||
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: 0.9724 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 85358 / Num. obs: 72050 / % possible obs: 84.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2 % / Rmerge(I) obs: 0.448 / Num. unique all: 7738 / % possible all: 87.4 |
Reflection | *PLUS Num. obs: 85358 / % possible obs: 98.7 % / Num. measured all: 461423 |
Reflection shell | *PLUS % possible obs: 90.4 % / Rmerge(I) obs: 0.366 |
-Processing
Software |
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Refinement | Resolution: 1.3→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_planar_d / Dev ideal: 0.024 |