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Yorodumi- PDB-2pws: Crystal structure of the complex formed between phospholipase A2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pws | ||||||
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Title | Crystal structure of the complex formed between phospholipase A2 and 2-(4-isobutyl-phenyl)-propionic acid at 2.2 A resolution | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE / NSAIDs / Active site / Inhibitor | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Kumar, S. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the complex formed between phospholipase A2 and 2-(4-isobutyl-phenyl)-propionic acid at 2.2 resolution Authors: Kumar, S. / Singh, N. / Sharma, S. / Kaur, P. / 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 | 2pws.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pws.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 2pws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/2pws ftp://data.pdbj.org/pub/pdb/validation_reports/pw/2pws | HTTPS FTP |
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-Related structure data
Related structure data | 1sv3S 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 / Fragment: phospholipase A2 / 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-IBP / |
#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: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: Ammonium Sulphate, PEG 4000, pH 6.8, VAPOR DIFFUSION, SITTING 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: Apr 22, 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: 2.21→53.45 Å / Num. all: 6829 / Num. obs: 6488 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.21→2.29 Å / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SV3 Resolution: 2.21→53.45 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.587 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.277 / ESU R Free: 0.205 / 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: 31.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.268 Å / Total num. of bins used: 20 /
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