[English] 日本語
Yorodumi- PDB-1p7o: Crystal structure of phospholipase A2 (MIPLA4) from Micropechis i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p7o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phospholipase A2 (MIPLA4) from Micropechis ikaheka | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / PHOSPHOLIPASE A2 / MICROPECHIS IKAHEKA / PANCREATIC LOOP | ||||||
Function / homology | Function and homology information phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Micropechis ikaheka (cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lok, S.M. / Swaminathan, K. | ||||||
Citation | Journal: FEBS J. / Year: 2005 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: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2001 Title: Purification and properties of three new phospholipase A2 isoenzymes from Micropechis ikaheka venom Authors: Gao, R. / Kini, R.M. / Li, G.D. / Luo, R.H. / Selvanayagam, Z.E. / Gopalakrishnakone, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1p7o.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1p7o.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 1p7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/1p7o ftp://data.pdbj.org/pub/pdb/validation_reports/p7/1p7o | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14048.985 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Micropechis ikaheka (cobra) / References: UniProt: Q45Z29*PLUS, phospholipase A2 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.79 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.1M ammonium sulphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99 Å / Num. all: 438899 / Num. obs: 438899 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.58 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.074 |
Reflection shell | Resolution: 2.06→2.14 Å / Redundancy: 6.26 % / Num. unique all: 6697 / Rsym value: 0.448 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MiPLA3 Resolution: 2.3→7.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 363337.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.5818 Å2 / ksol: 0.552345 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→7.99 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|