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Yorodumi- PDB-1gh4: Structure of the triple mutant (K56M, K120M, K121M) of phospholip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gh4 | ||||||
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Title | Structure of the triple mutant (K56M, K120M, K121M) of phospholipase A2 | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / Alpha Helix / Beta Sheet / Triple 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 / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...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 / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / 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 / Resolution: 1.9 Å | ||||||
Authors | Sekar, K. / Velmurugan, D. / Tsai, M.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2. Authors: Rajakannan, V. / Yogavel, M. / Poi, M.J. / Jeyaprakash, A.A. / Jeyakanthan, J. / Velmurugan, D. / Tsai, M.D. / Sekar, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gh4.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gh4.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/1gh4 ftp://data.pdbj.org/pub/pdb/validation_reports/gh/1gh4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 13816.551 Da / Num. of mol.: 1 / Mutation: K56M,K120M,K121M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P00593, phospholipase A2 | ||||
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#2: Chemical | #3: Chemical | ChemComp-MPD / ( | #4: 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: 2.26 Å3/Da / Density % sol: 45.59 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion method / pH: 7.2 Details: Tris Buffer, MPD, 70% MPD reservoir, 17-20Mg/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 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 2000 |
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→14.2 Å / Num. all: 8880 / Num. obs: 8880 / % possible obs: 88 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.293 / Num. unique all: 910 / % possible all: 72 |
Reflection | *PLUS % possible obs: 88.3 % / Num. measured all: 40817 |
-Processing
Software |
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Refinement | Resolution: 1.9→14.2 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→14.2 Å
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Refine LS restraints | Type: protein_rep.param / Dev ideal: 0.011 | ||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 14.2 Å / σ(F): 0 / Rfactor obs: 0.196 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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