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Yorodumi- PDB-1sv9: Crystal structure of the complex formed between groupII phospholi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sv9 | ||||||
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Title | Crystal structure of the complex formed between groupII phospholipase A2 and anti-inflammatory agent 2-[(2,6-Dichlorophenyl)amino] benzeneacetic acid at 2.7A resolution | ||||||
Components | Phospholipase A2 | ||||||
Keywords | TOXIN / Phospholipase A2 / complex / diclofenac / 2.7A resolution | ||||||
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 russellii (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Senthil kumar, R. / Singh, N. / Ethayathulla, A.S. / Prem kumar, R. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the complex formed between group II phospholipase A2 and anti-inflammatory agent 2-[(2,6-Dichlorophenyl)amino] benzeneacetic acid at 2.7A resolution Authors: Senthil kumar, R. / Singh, N. / Ethayathulla, A.S. / Prem kumar, R. / Sharma, S. / 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 | 1sv9.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sv9.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/1sv9 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/1sv9 | HTTPS FTP |
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-Related structure data
Related structure data | 1fb2S 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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Details | The biological Unit is Monomer |
-Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Secretion: venom / Species: Daboia russellii / Strain: russellii / References: UniProt: P59071, phospholipase A2 |
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#2: Chemical | ChemComp-DIF / |
#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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-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: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 2004 / 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: 2.7→20 Å / Num. all: 3463 / Num. obs: 3463 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.41 % / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.119 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.7→2.76 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.206 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FB2 Resolution: 2.71→18.76 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 774739.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.2549 Å2 / ksol: 0.334156 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.71→18.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.083 / Total num. of bins used: 6
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Xplor file |
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