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Yorodumi- PDB-1bjj: AGKISTRODOTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bjj | ||||||
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Title | AGKISTRODOTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN FROM AGKISTRODON HALYS PALLAS | ||||||
Components | AGKISTRODOTOXIN | ||||||
Keywords | PRESYNAPTIC NEUROTOXIN / PHOSPHOLIPASE A2 / HYDROLASE | ||||||
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 | Gloydius halys (Halys viper) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tang, L. / Zhou, Y. / Lin, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of agkistrodotoxin in an orthorhombic crystal form with six molecules per asymmetric unit. Authors: Tang, L. / Zhou, Y.C. / Lin, Z.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bjj.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bjj.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/1bjj ftp://data.pdbj.org/pub/pdb/validation_reports/bj/1bjj | HTTPS FTP |
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-Related structure data
Related structure data | 1a2aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 14013.746 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: THE SNAKE IS ALSO NAMED AGKISTRODON BLOMHOFFII BREVICAUDUS Source: (natural) Gloydius halys (Halys viper) / Secretion: VENOM / References: UniProt: P14421, phospholipase A2 #2: Chemical | ChemComp-CA / #3: 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: 3.06 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 24339 / % possible obs: 93.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.169 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 2.67 % / Rsym value: 0.546 / % possible all: 92.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. measured all: 71221 / Rmerge(I) obs: 0.169 |
Reflection shell | *PLUS % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A2A Resolution: 2.8→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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