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Yorodumi- PDB-2zbh: Crystal structure of the complex of phospholipase A2 with Bavacha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zbh | ||||||
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Title | Crystal structure of the complex of phospholipase A2 with Bavachalcone from Aerva lanata at 2.6 A resolution | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE / complex / Daucosterol / Aerva lanata / phospholipse A2 / Calcium / Lipid degradation / Metal-binding / Neurotoxin / Presynaptic neurotoxin / Secreted / Toxin | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kumar, S. / Damodar, N.C. / Jain, R. / Singh, N. / Sharma, S. / Kaur, P. / Haridas, M. / Srinivasan, A. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the complex of phospholipase A2 with Bavachalcone from Aerva lanata at 2.6 A resolution Authors: Kumar, S. / Damodar, N.C. / Jain, R. / Singh, N. / Sharma, S. / Kaur, P. / Haridas, 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 | 2zbh.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zbh.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zbh ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zbh | HTTPS FTP |
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-Related structure data
Related structure data | 2qvdS 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: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2 |
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#2: Chemical | ChemComp-BVL / ( |
#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: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 50mm Ammonium acetate, 0.2M ammonium sulphate, 30%PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 18, 2007 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→17.87 Å / Num. obs: 4094 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 50.4 Å2 / Rsym value: 0.126 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 19057 / Rsym value: 0.482 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QVD Resolution: 2.6→17.87 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 55110.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4875 Å2 / ksol: 0.309582 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→17.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
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Xplor file |
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