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Yorodumi- PDB-1g2x: Sequence induced trimerization of krait PLA2: crystal structure o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2x | ||||||
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Title | Sequence induced trimerization of krait PLA2: crystal structure of the trimeric form of krait PLA2 | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | TOXIN / Phospholipase A2 / Homotrimer / Bungarus caeruleus | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bungarus caeruleus (cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Singh, G. / Gourinath, S. / Sharma, S. / Bhanumathi, S. / Paramsivam, M. / Singh, T.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Sequence-induced trimerization of phospholipase A2: structure of a trimeric isoform of PLA2 from common krait (Bungarus caeruleus) at 2.5 A resolution. Authors: Singh, G. / Gourinath, S. / Saravanan, K. / Sharma, S. / Bhanumathi, S. / Betzel, C.h. / Srinivasan, A. / Singh, T.P. #1: Journal: To be Published Title: Specific mutations in Krait PLA2 lead to dimerization of protein molecules: Crystal structure of Krait PLA2 at 2.1 resolution. Authors: Gourinath, S. / Singh, G. / Sharma, S. / Bhanumathi, S. / Betzel, C. / Paramsivam, M. / Srinivasan, A. / Singh, T.P. #2: Journal: To be Published Title: Three-dimensional structure of a novel phospholipase A2 from Indian common krait at 2.45 resolution. Authors: Singh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / 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 | 1g2x.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2x.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 1g2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2x ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2x | HTTPS FTP |
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-Related structure data
Related structure data | 1fe5S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12984.620 Da / Num. of mol.: 3 / Fragment: RESIDUES 28-145 / Source method: isolated from a natural source / Details: NATURAL PROTEIN-ISOFORM / Source: (natural) Bungarus caeruleus (cobra) / Secretion: VENOM References: UniProt: Q9DF52, UniProt: Q6SLM0*PLUS, phospholipase A2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM Tris.HCl, 3.0 M NaCl, 1mM NaN3, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 281.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 281 K / pH: 8.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 12779 / Num. obs: 12745 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.98 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.091 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 4.98 % / Num. unique all: 12779 / Rsym value: 0.203 / % possible all: 99.6 |
Reflection | *PLUS Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1FE5 Resolution: 2.5→14.28 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 13123.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.03 Å2 / ksol: 0.472 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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