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Yorodumi- PDB-3p2p: ENHANCED ACTIVITY AND ALTERED SPECIFICITY OF PHOSPHOLIPASE A2 BY ... -
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-Basic information
Entry | Database: PDB / ID: 3p2p | ||||||
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Title | ENHANCED ACTIVITY AND ALTERED SPECIFICITY OF PHOSPHOLIPASE A2 BY DELETION OF A SURFACE LOOP | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE(CARBOXYL 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 MAP kinase activity / positive regulation of interleukin-8 production / cellular response to insulin stimulus / phospholipid binding / 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 / positive regulation of cell population proliferation / calcium ion binding / 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: 2.1 Å | ||||||
Authors | Dijkstra, B.W. / Thunnissen, M.M.G.M. / Kalk, K.H. / Drenth, J. | ||||||
Citation | Journal: Science / Year: 1989 Title: Enhanced activity and altered specificity of phospholipase A2 by deletion of a surface loop. Authors: Kuipers, O.P. / Thunnissen, M.M. / de Geus, P. / Dijkstra, B.W. / Drenth, J. / Verheij, H.M. / de Haas, G.H. #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: 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. #3: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of Bovine Pancreatic Phospholipase A2 at 1.7 Angstroms Resolution Authors: Dijkstra, B.W. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #4: Journal: Nature / Year: 1981 Title: Active Site and Catalytic Mechanism of Phospholipase A2 Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. #5: Journal: J.Mol.Biol. / Year: 1978 Title: Three-Dimensional Structure and Disulfide Bond Connections in Bovine Pancreatic Phospholipase A2 Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. / Vandermaelen, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p2p.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p2p.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p2p_validation.pdf.gz | 376.1 KB | Display | wwPDB validaton report |
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Full document | 3p2p_full_validation.pdf.gz | 392.8 KB | Display | |
Data in XML | 3p2p_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 3p2p_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/3p2p ftp://data.pdbj.org/pub/pdb/validation_reports/p2/3p2p | HTTPS FTP |
-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: SEE REMARK 6. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.311854, -0.931273, -0.188355), Vector: Details | THE ENZYME CRYSTALLIZES WITH A DIMER IN THE ASYMMETRIC UNIT. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW CAN BE APPLIED TO SUBUNIT 2 (CHAIN *B*) TO OBTAIN OPTIMAL SUPERPOSITION OF C-ALPHA COORDINATES ON THOSE OF SUBUNIT 1 (CHAIN *A*). THE RMS DIFFERENCE FOR ALL 119 CARBON-ALPHA PAIRS IS 0.542 ANGSTROMS. | |
-Components
#1: Protein | Mass: 13397.018 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 / | Nonpolymer details | CALCIUM CA B 2 IS BOUND BETWEEN THE *A* AND *B* CHAINS. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.74 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / % possible obs: 88.5 % |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.186 / Highest resolution: 2.1 Å | ||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor obs: 0.237 / Rfactor Rwork: 0.237 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: bond_d / Dev ideal: 0.009 |