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Yorodumi- PDB-1tp2: Crystal structure of the complex of group II phospholipaseA2 dime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tp2 | ||||||
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Title | Crystal structure of the complex of group II phospholipaseA2 dimer with a fatty acid tridecanoic acid at 2.4 A resolution | ||||||
Components | Phospholipase A2 VRV-PL-VIIIa | ||||||
Keywords | HYDROLASE / Catalysis / Inhibition / Fatty acid | ||||||
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: 2.4 Å | ||||||
Authors | Singh, N. / Jabeen, T. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the complex of group II phospholipaseA2 dimer with a fatty acid tridecanoic acid at 2.4 A resolution Authors: Singh, N. / Jabeen, T. / 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 | 1tp2.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tp2.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/1tp2 ftp://data.pdbj.org/pub/pdb/validation_reports/tp/1tp2 | 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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-Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: venom / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2 #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | ChemComp-ACY / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 20mM Sodium acetate, Calcium chloride, 15% PEG8000, 0.2M Ammonium sulphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 2002 / 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: 2.4→20 Å / Num. all: 7984 / Num. obs: 7984 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.9 Å2 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FB2 Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 173506.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9321 Å2 / ksol: 0.344077 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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