+Open data
-Basic information
Entry | Database: PDB / ID: 1jlt | ||||||
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Title | Vipoxin Complex | ||||||
Components |
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Keywords | HYDROLASE / HETERODIMER COMPLEX / PHOSPHOLIPASE / VIPOXIN / PLA2-ACTIVITY | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / killing of cells of another organism / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Vipera ammodytes ammodytes (western sand viper) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Banumathi, S. / Rajashankar, K.R. / Notzel, C. / Aleksiev, B. / Singh, T.P. / Genov, N. / Betzel, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of the neurotoxic complex vipoxin at 1.4 A resolution. Authors: Banumathi, S. / Rajashankar, K.R. / Notzel, C. / Aleksiev, B. / Singh, T.P. / Genov, N. / Betzel, C. | ||||||
History |
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Remark 999 | sequence The authors' residue numbering is not sequential. Residue numbers 15, 57, 60, 62-67, 87, ...sequence The authors' residue numbering is not sequential. Residue numbers 15, 57, 60, 62-67, 87, 123 are not used in the coordinates. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jlt.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jlt.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jlt ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jlt | HTTPS FTP |
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-Related structure data
Related structure data | 1aokS 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
#1: Protein | Mass: 13664.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Vipera ammodytes ammodytes (western sand viper) Species: Vipera ammodytes / Strain: ammodytes / References: UniProt: P04084 |
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#2: Protein | Mass: 13846.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence homology between phospholipase and its inhibitor in snake venom. The primary structure of phospholipase A2 of vipoxin from the venom of the Bulgarian viper (Vipera ammodytes ammodytes, Serpentes) Source: (natural) Vipera ammodytes ammodytes (western sand viper) Species: Vipera ammodytes / Strain: ammodytes / References: UniProt: P14420, phospholipase A2 |
#3: Chemical | ChemComp-MRD / ( |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG 4000, MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 287 K | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.908 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: Collimator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→20 Å / Num. all: 54019 / Num. obs: 53423 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4 / Num. unique all: 2525 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 96.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AOK Resolution: 1.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT Details: used maximum likelihood target using amplitudes procedure
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Displacement parameters | Biso mean: 15.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.08 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.182 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.7 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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