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Yorodumi- PDB-1yxh: Crystal structure of a novel phospholipase A2 from Naja naja sagi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yxh | ||||||
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Title | Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong anticoagulant activity | ||||||
Components | phospholipase A2 | ||||||
Keywords | HYDROLASE / PLA2 / anticoagulation / monomer | ||||||
Function / homology | Function and homology information phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Naja sagittifera (cobra) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Jabeen, T. / Singh, N. / Singh, R.K. / Sharma, S. / Srinivasan, A. / Singh, T.P. | ||||||
Citation | Journal: Toxicon / Year: 2005 Title: Crystal structure of a novel phospholipase A(2) from Naja naja sagittifera with a strong anticoagulant activity Authors: Jabeen, T. / Singh, N. / Singh, R.K. / Ethayathulla, A.S. / Sharma, S. / Srinivasan, A. / 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 | 1yxh.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yxh.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yxh_validation.pdf.gz | 385.4 KB | Display | wwPDB validaton report |
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Full document | 1yxh_full_validation.pdf.gz | 386.5 KB | Display | |
Data in XML | 1yxh_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1yxh_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/1yxh ftp://data.pdbj.org/pub/pdb/validation_reports/yx/1yxh | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 14211.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / References: UniProt: Q6T179, phospholipase A2 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | #5: 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: 2.2 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10mM phosphate buffer, 2mM CaCl2, 25% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 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: 1.86→42.64 Å / Num. all: 49325 / Num. obs: 9822 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.86→1.9 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.455 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.862→1.91 Å / Total num. of bins used: 20 /
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