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Yorodumi- PDB-2pb8: Crystal structure of the complex formed between phospholipase A2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pb8 | ||||||
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Title | Crystal structure of the complex formed between phospholipase A2 and peptide Ala-Val-Tyr-Ser at 2.0 A resolution | ||||||
Components |
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Keywords | HYDROLASE / Inhibitor | ||||||
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 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 peptide Ala-Val-Tyr-Ser at 2.0 A 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 | 2pb8.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pb8.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/2pb8 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/2pb8 | 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 / 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: Protein/peptide | Mass: 438.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized | ||
#3: Chemical | #4: 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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Acetate, 30% PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 292 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: Mar 10, 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→53.45 Å / Num. all: 8734 / Num. obs: 8317 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SV3 Resolution: 2→53.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.484 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 31.964 Å2
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Refinement step | Cycle: LAST / Resolution: 2→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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