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Yorodumi- PDB-3f97: Crystal structure of human plasma platelet activating factor acet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f97 | ||||||
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Title | Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by soman | ||||||
Components | Platelet-activating factor acetylhydrolase | ||||||
Keywords | HYDROLASE / PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / SECRETED PROTEIN / ALPHA/BETA-HYDROLASE-FOLD / LDL-BOUND / LIPOPROTEIN ASSOCIATED PHOSPHOLIPASE A2 / LP-PLA2 / GROUP VIIA PLA2 / GLYCOPROTEIN / LIPID DEGRADATION / POLYMORPHISM / SOMAN / Disease mutation / Secreted | ||||||
Function / homology | Function and homology information plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / peptide hormone processing / hydrolase activity, acting on ester bonds / Synthesis, secretion, and deacylation of Ghrelin / lipid oxidation / phospholipid binding / positive regulation of inflammatory response / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Samanta, U. / Bahnson, B.J. | ||||||
Citation | Journal: Biochem Pharmacol / Year: 2009 Title: Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes. Authors: Samanta, U. / Kirby, S.D. / Srinivasan, P. / Cerasoli, D.M. / Bahnson, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f97.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f97.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f97_validation.pdf.gz | 465.1 KB | Display | wwPDB validaton report |
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Full document | 3f97_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 3f97_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 3f97_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/3f97 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/3f97 | HTTPS FTP |
-Related structure data
Related structure data | 3f96C 3f98C 3f9cC 3d59S S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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-Components
#1: Protein | Mass: 43494.367 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 47-429 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G7, PAFAH / Production host: Escherichia coli (E. coli) References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 48.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PH 6.6, pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2006 / Details: ROSENBAUM-ROCK |
Radiation | Monochromator: SI(111) 0.990 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 87071 / Num. obs: 87071 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.97 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.36 / % possible all: 73.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE STRUCTURE, PDB ENTRY 3D59 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.768 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.746 Å / Total num. of bins used: 20
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