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Yorodumi- PDB-2phi: A LARGE CONFORMATIONAL CHANGE IS FOUND IN THE CRYSTAL STRUCTURE O... -
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-Basic information
Entry | Database: PDB / ID: 2phi | ||||||
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Title | A LARGE CONFORMATIONAL CHANGE IS FOUND IN THE CRYSTAL STRUCTURE OF THE PORCINE PANCREATIC PHOSPHOLIPASE A2 POINT MUTANT F63V | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE (CARBOXYLIC ESTER) | ||||||
Function / homology | Function and homology information positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding ...positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of MAP kinase activity / phospholipid binding / fatty acid biosynthetic process / cellular response to insulin stimulus / positive regulation of immune response / positive regulation of fibroblast proliferation / 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 / Resolution: 2.2 Å | ||||||
Authors | Dijkstra, B.W. / Thunnissen, M.M.G.M. / Kalk, K.H. / Drenth, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Crystal structure of a porcine pancreatic phospholipase A2 mutant. A large conformational change caused by the F63V point mutation. Authors: Thunnissen, M.M. / Franken, P.A. / de Haas, G.H. / Drenth, J. / Kalk, K.H. / Verheij, H.M. / Dijkstra, B.W. #1: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Angstroms Resolution and Comparison with Bovine Phospholipase A2 Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #2: Journal: FEBS Lett. / Year: 1983 Title: Polypeptide Chains with Similar Amino Acid Sequences But a Distinctly Different Conformation. Bovine and Porcine Phospholipase A2 Authors: Dijkstra, B.W. / Weijer, W.J. / Wierenga, R.K. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1982 Title: The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Angstroms Resolution Authors: Dijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2phi.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2phi.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 2phi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2phi ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2phi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CALCIUM 1 LIES ON A NONCRYSTALLOGRAPHIC LOCAL TWO-FOLD AXIS. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998134, 0.005944, -0.060766), Vector: Details | THE ENZYME CRYSTALLIZES AS A DIMER IN THE ASYMMETRIC UNIT. THE TRANSFORMATION GIVEN ON *MTRIX* RECORDS BELOW YIELDS OPTIMAL CARBON-ALPHA COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE RMS DIFFERENCE FOR ALL 124 CARBON-ALPHA PAIRS IS 0.526 ANGSTROMS, 0.153 FOR THE 93 CARBON-ALPHA PAIRS WHEN THE MOST DEVIATING PAIRS ARE REMOVED. | |
-Components
#1: Protein | Mass: 13961.671 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00592, phospholipase A2 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.176 / Highest resolution: 2.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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