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- PDB-1pwo: Crystal Structure of Phospholipase A2 (MIPLA2) from Micropechis I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pwo | ||||||
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Title | Crystal Structure of Phospholipase A2 (MIPLA2) from Micropechis Ikaheka | ||||||
![]() | Phospholipase A2 | ||||||
![]() | HYDROLASE / Phospholipase A2 / Micropechis Ikaheka / Pancreatic Loop | ||||||
Function / homology | Phospholipase A2 / Phospholipase A2 domain / Up-down Bundle / Mainly Alpha![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lok, S.M. / Swaminathan, K. | ||||||
![]() | ![]() Title: Structure and function comparison of Micropechis ikaheka snake venom phospholipase A2 isoenzymes. Authors: Lok, S.M. / Gao, R. / Rouault, M. / Lambeau, G. / Gopalakrishnakone, P. / Swaminathan, K. #1: ![]() Title: Purification and properties of three new phospholipase A2 isoenzymes from Micropechis ikaheka venom. Authors: Gao, R. / Kini, R.M. / Li, G. / Luo, R. / Selvanayagam, Z.E. / Gopalakrishnakone, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.8 KB | Display | ![]() |
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PDB format | ![]() | 88.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
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Full document | ![]() | 474.4 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13983.006 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 2.4M Ammonium Sulphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jan 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 25377 / Num. obs: 22385 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 37.6 Å2 / Rsym value: 0.054 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 4.52 / Num. unique all: 2491 / Rsym value: 0.211 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MiPLA4 Resolution: 2.6→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 540537.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.7729 Å2 / ksol: 0.486051 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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