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Yorodumi- PDB-1fe5: SEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fe5 | ||||||
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Title | SEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM COMMON KRAIT (BUNGARUS CAERULEUS) AT 2.4 RESOLUTION: IDENTIFICATION AND CHARACTERIZATION OF ITS PHARMACOLOGICAL SITES. | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | TOXIN / Bungarus caeruleus / phospholipase A2 (PLA2) / presynaptic neurotoxin / neurotoxic site / X-ray structure / molecular replacement | ||||||
Function / homology | Function and homology information phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bungarus caeruleus (cobra) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.45 Å | ||||||
Authors | Singh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites. Authors: Singh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fe5.cif.gz | 32.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fe5.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fe5_validation.pdf.gz | 368.9 KB | Display | wwPDB validaton report |
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Full document | 1fe5_full_validation.pdf.gz | 370.3 KB | Display | |
Data in XML | 1fe5_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1fe5_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/1fe5 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/1fe5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Phospholipase A2 monomer in each assymetric unit |
-Components
#1: Protein | Mass: 12990.490 Da / Num. of mol.: 1 / Fragment: NATURAL PROTEIN / Source method: isolated from a natural source / Source: (natural) Bungarus caeruleus (cobra) / Secretion: VENOM / References: UniProt: Q9DF52, 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: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: Ammonium sulphate, CaCl2, Dioxane, Sodium cacodylate , pH 7.0, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 8 ℃ / pH: 8.5 / Method: vapor diffusion, sitting 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: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→15 Å / Num. all: 79758 / Num. obs: 4629 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.223 / Num. unique all: 521 / % possible all: 70.7 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.9 Å / % possible obs: 92 % / Rmerge(I) obs: 0.174 |
-Processing
Software |
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Refinement | Resolution: 2.45→9.99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 151511.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.46 Å2 / ksol: 0.405 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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