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Open data
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Basic information
Entry | Database: PDB / ID: 1qll | ||||||
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Title | Piratoxin-II (Prtx-II) - a K49 PLA2 from Bothrops pirajai | ||||||
![]() | PHOSPHOLIPASE A2 | ||||||
![]() | NEUROTOXIN / K49 PHOSPHOLIPASE A2 (PLA2) | ||||||
Function / homology | ![]() calcium-dependent phospholipase A2 activity / arachidonate 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, W.-H. / Polikarpov, I. | ||||||
![]() | ![]() Title: Structural Basis for Low Catalytic Activity in Lys49 Phospholipases A2-A Hypothesis: The Crystal Structure of Piratoxin II Complexed to Fatty Acid Authors: Lee, W.H. / Da Silva Giotto, M.T. / Marangoni, S. / Toyama, M.H. / Polikarpov, I. / Garratt, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1clpS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, -0.0003, -0.0043), Vector: Details | THE ASYMMETRIC UNIT CONTAINS A HOMO-DIMERIC COMPLEX | |
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Components
#1: Protein | Mass: 13784.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FATTY ACID TRAPPED AT THE HYDROPHOBIC CHANNEL / Source: (natural) ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | THE PHOSPHOLIPASES A2 (PLA2) CAN BE DIVIDED INTO TWO MAJOR CLASSES BASED UPON CATALYTIC ACTIVITY. ...THE PHOSPHOLIP | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 28% PEG 3350, 0.25 M LITHIUM SULFATE 0.1 M TRIS-HCL PH 8.5, AT 277 K FOR APPROX. 40 DAYS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→20 Å / Num. obs: 6934 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 3.43 % / Rsym value: 0.07 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 1.53 % / Mean I/σ(I) obs: 2.57 / Rsym value: 0.26 / % possible all: 72.5 |
Reflection | *PLUS Num. measured all: 23809 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 72.5 % / Rmerge(I) obs: 0.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CLP Resolution: 2.04→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE C-TERMINAL IS CLEARLY VISIBLE IN THE DENSITY MAP AND IT IS MAKING A DISULPHIDE BRIDGE.
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Refinement step | Cycle: LAST / Resolution: 2.04→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |