[English] 日本語
Yorodumi- PDB-1fb2: STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fb2 | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | TOXIN / Phospholipase A2 / Daboia Russelli Pulchella / Neurotoxic | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / 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 | Daboia russellii pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Chandra, V. / Kaur, P. / Betzel, C. / Singh, T.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution. Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C. / Singh, T.P. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Three-Dimensional Structure of a Presynaptic Neurotoxic Phospholipase A2 from Daboia Russelli pulchella at 2.4 Resolution Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / P Singh, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fb2.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fb2.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/1fb2 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/1fb2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1cl5S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 / Keywords: NATIVE / References: UniProt: P59071 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20mM Sodium Cacodylate, 1.4M Ammonium Sulphate, 4mM Calcium Chloride, 3% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 180 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→24.1 Å / Num. all: 19822 / Num. obs: 18001 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.026 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1913 / Rsym value: 0.165 / % possible all: 98.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 17922 / % possible obs: 91 % / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.163 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CL5 Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used restrained least-squares refinement procedure
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.9 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.216 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|