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Yorodumi- PDB-1bwr: PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bwr | ||||||
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Title | PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE | ||||||
Components | PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE1-alkyl-2-acetylglycerophosphocholine esterase | ||||||
Keywords | HYDROLASE / ACETYLHYDROLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ho, Y.S. / Sheffield, P.J. / Masuyama, J. / Arai, H. / Li, J. / Aoki, J. / Inoue, K. / Derewenda, U. / Derewenda, Z. | ||||||
Citation | Journal: Protein Eng. / Year: 1999 Title: Probing the Substrate Specificity of the Intracellular Brain Platelet-Activating Factor Acetylhydrolase Authors: Ho, Y.S. / Sheffield, P.J. / Masuyama, J. / Arai, H. / Li, J. / Aoki, J. / Inoue, K. / Derewenda, U. / 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 | 1bwr.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bwr.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bwr ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bwr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25986.453 Da / Num. of mol.: 1 / Mutation: T103S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: BRAIN / Organ: BRAIN / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 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: 2 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||
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Crystal grow | pH: 6.8 / Details: pH 6.8 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MSC MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 10257 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rsym value: 0.041 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Rsym value: 0.161 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PAF ACETYLHYDROLASE Resolution: 2.4→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 35.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_planar_d / Dev ideal: 0.035 |