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Yorodumi- PDB-1y6o: Crystal structure of disulfide engineered porcine pancreatic phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y6o | ||||||
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Title | Crystal structure of disulfide engineered porcine pancreatic phospholipase A2 to group-X isozyme in complex with inhibitor MJ33 and phosphate ions | ||||||
Components | Phospholipase A2, major isoenzyme | ||||||
Keywords | HYDROLASE / Hydrolase. Disulfide engineered PLA2. Porcine pancratic isozyme. | ||||||
Function / homology | Function and homology information Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / phospholipid binding / positive regulation of MAP kinase activity / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of immune response / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yu, B.Z. / Pan, Y.H. / Jassen, M.J.W. / Bahnson, B.J. / Jain, M.K. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Kinetic and structural properties of disulfide engineered phospholipase a(2): insight into the role of disulfide bonding patterns. Authors: Yu, B.Z. / Pan, Y.H. / Janssen, M.J.W. / Bahnson, B.J. / Jain, M.K. #1: Journal: Eur.J.Biochem. / Year: 1999 Title: Engineeering the disulphide bond patterns of secretory phospolipases A2 into porcine pancratic isozyme. The effects on folding, stability and enzymatic properties Authors: Janssen, M.J. / Verheij, H.M. / Slotboom, A.J. / Egmond, M.R. #2: Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of human group X secreted phospholipase A2. Electrostatically neutral interfacial surface targets zwitterionic membranes Authors: Pan, Y.H. / Yu, B.Z. / Singer, A.G. / Ghomashchi, F. / Lambeau, G. / Jain, M.K. / Bahnson, B.J. | ||||||
History |
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Remark 999 | SEQUENCE C-terminal extension (residues 125-131) KGESDKC were added to model the disulfide bonding ...SEQUENCE C-terminal extension (residues 125-131) KGESDKC were added to model the disulfide bonding pattern of the group X enzyme. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y6o.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y6o.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 1y6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y6o ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y6o | HTTPS FTP |
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-Related structure data
Related structure data | 1y6pC 1fxfS C: citing same article (ref.) S: Starting model for refinement |
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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 | The asymmetric unit contains two biological units: chain A and B. |
-Components
#1: Protein | Mass: 14712.515 Da / Num. of mol.: 2 / Mutation: M8L,M20L, N50C, c-terminal insertion KGESDKC Source method: isolated from a genetically manipulated source Details: M8L,M20L, N50C, c-termial insertion KGESDKC (residues 125 to 131) Source: (gene. exp.) Sus scrofa (pig) / Gene: PLA2G1B / Plasmid: pMAR25 / Production host: Escherichia coli (E. coli) / Strain (production host): PC2429 Keywords: M8L,M20L, N50C, c-termial insertion KGESDKC (residues 125 to 131) References: UniProt: P00592, phospholipase A2 #2: Chemical | #3: Chemical | ChemComp-PO4 / #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: 2.45 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Potassium phosphate, PEG 8000, , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2001 / Details: Mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.6 Å / Num. all: 16950 / Num. obs: 14222 / % possible obs: 83.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.045 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1398 / Rsym value: 0.293 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FXF Resolution: 2→28.64 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 427212.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Atoms C2-C16 in residue 217 and atoms C4-C16 in residue 218 were deleted from the model due to disorder.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.2197 Å2 / ksol: 0.383718 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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