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Yorodumi- PDB-1g4i: Crystal structure of the bovine pancreatic phospholipase A2 at 0.97A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g4i | ||||||
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Title | Crystal structure of the bovine pancreatic phospholipase A2 at 0.97A | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / Lipid degradation | ||||||
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 / SYNCHROTRON / Resolution: 0.97 Å | ||||||
Authors | Steiner, R.A. / Rozeboom, H.J. / de Vries, A. / Kalk, K.H. / Murshudov, G.N. / Wilson, K.S. / Dijkstra, B.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution. Authors: Steiner, R.A. / Rozeboom, H.J. / de Vries, A. / Kalk, K.H. / Murshudov, G.N. / Wilson, K.S. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g4i.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g4i.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/1g4i ftp://data.pdbj.org/pub/pdb/validation_reports/g4/1g4i | HTTPS FTP |
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-Related structure data
Related structure data | 1uneS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13810.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00593, phospholipase A2 |
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-Non-polymers , 5 types, 254 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Chemical | #6: 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: 2.01 Å3/Da / Density % sol: 38.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 7.6 Details: MPD, calcium chloride, Tris buffer, pH 7.6, SMALL TUBES, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.67 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 25, 1999 |
Radiation | Monochromator: 2 crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.67 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→20 Å / Num. all: 66635 / Num. obs: 66635 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.04 % / Biso Wilson estimate: 6.373 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 0.97→0.99 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.89 / % possible all: 97.4 |
Reflection | *PLUS Num. measured all: 469197 |
Reflection shell | *PLUS % possible obs: 97.4 % |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1UNE Resolution: 0.97→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 0.97→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 63381 / Num. reflection Rfree: 3372 / Rfactor Rfree: 0.1139 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |