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Yorodumi- PDB-2qvd: Identification of a potent anti-inflammatory agent from the natur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qvd | ||||||
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Title | Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / phospholipids / membrane / hydrolysis / inhibitor / plant extraxt / Lipid degradation / Metal-binding / Neurotoxin / Presynaptic neurotoxin / Secreted / Toxin / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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: 1.93 Å | ||||||
Authors | Kumar, S. / Chandra, D.N. / Singh, N. / Jithesh, O. / Sharma, S. / Haridas, M. / Singh, T.P. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2011 Title: Identification of a novel and potent inhibitor of phospholipase A(2) in a medicinal plant: crystal structure at 1.93A and Surface Plasmon Resonance analysis of phospholipase A(2) complexed with berberine Authors: Chandra, D.N. / Prasanth, G.K. / Singh, N. / Kumar, S. / Jithesh, O. / Sadasivan, C. / Sharma, S. / Singh, T.P. / Haridas, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qvd.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qvd.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvd ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvd | HTTPS FTP |
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-Related structure data
Related structure data | 2pycS 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) / References: UniProt: P59071, phospholipase A2 |
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#2: Chemical | ChemComp-BER / |
#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: 2.52 Å3/Da / Density % sol: 51.23 % |
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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: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54132 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 2, 2007 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54132 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→53.45 Å / Num. all: 10240 / Num. obs: 9715 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.93→2 Å / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PYC Resolution: 1.93→53.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.75 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.155 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20 /
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