+Open data
-Basic information
Entry | Database: PDB / ID: 1c74 | ||||||
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Title | Structure of the double mutant (K53,56M) of phospholipase A2 | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / Alpha Helix / Beta Sheet / Double mutant | ||||||
Function / homology | Function and homology information Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sekar, K. / Tsai, M.D. / Jain, M.K. / Ramakumar, S. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structural basis of the anionic interface preference and k*cat activation of pancreatic phospholipase A2. Authors: Yu, B.Z. / Poi, M.J. / Ramagopal, U.A. / Jain, R. / Ramakumar, S. / Berg, O.G. / Tsai, M.D. / Sekar, K. / Jain, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c74.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c74.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c74 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c74 | HTTPS FTP |
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-Related structure data
Related structure data | 1mktS 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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Unit cell |
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-Components
#1: Protein | Mass: 13814.536 Da / Num. of mol.: 1 / Mutation: K53M, K56M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Description: PANCREAS / Gene: MATURE PLA2 / Organ: PANCREAS / Plasmid: PTO-A2MBL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P00593, phospholipase A2 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion method / pH: 7.2 Details: Tris Buffer, MPD, 50% MPD reservoir, 15Mg/ml protein, 5 mM CaCl2, pH 7.2, vapor diffusion method, temperature 293.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. all: 9733 / Num. obs: 9733 / % possible obs: 89 % / Redundancy: 4.32 % / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.333 / Num. unique all: 857 / % possible all: 71 |
Reflection | *PLUS Num. measured all: 42068 |
Reflection shell | *PLUS % possible obs: 71 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MKT Resolution: 1.9→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: x-plor / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints | Type: x_bond_d / Dev ideal: 0.011 | |||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: parhcsdx.pro | |||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 8033 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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