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- PDB-1aho: THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPIO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aho | ||||||
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Title | THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN | ||||||
![]() | TOXIN II | ||||||
![]() | NEUROTOXIN / TOXIN II / SCORPION / AB INITIO PHASING | ||||||
Function / homology | ![]() sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Smith, G.D. / Blessing, R.H. / Ealick, S.E. / Fontecilla-Camps, J.C. / Hauptman, H.A. / Housset, D. / Langs, D.A. / Miller, R. | ||||||
![]() | ![]() Title: Ab initio structure determination and refinement of a scorpion protein toxin. Authors: Smith, G.D. / Blessing, R.H. / Ealick, S.E. / Fontecilla-Camps, J.C. / Hauptman, H.A. / Housset, D. / Langs, D.A. / Miller, R. #1: ![]() Title: Crystal Structure of Toxin II from the Scorpion Androctonus Australis Hector Refined at 1.3 A Resolution Authors: Housset, D. / Habersetzer-Rochat, C. / Astier, J.P. / Fontecilla-Camps, J.C. #2: ![]() Title: Orthorhombic Crystals and Three-Dimensional Structure of the Potent Toxin II from the Scorpion Androctonus Australis Hector Authors: Fontecilla-Camps, J.C. / Habersetzer-Rochat, C. / Rochat, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.7 KB | Display | ![]() |
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PDB format | ![]() | 24.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399 KB | Display | ![]() |
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Full document | ![]() | 399 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7262.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 36.43 % |
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Crystal grow | pH: 6.8 / Details: pH 6.8 |
Crystal grow | *PLUS Method: other / Details: none |
-Data collection
Diffraction | Mean temperature: 287 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1994 / Details: NA | |||||||||
Radiation | Monochromator: NA / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 0.964→16 Å / Num. obs: 31001 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 7.23 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.7 | |||||||||
Reflection shell | Resolution: 0.96→0.99 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.3 / % possible all: 80 | |||||||||
Reflection shell | *PLUS % possible obs: 75.6 % |
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Processing
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 0.96→8 Å / σ(F): 2 Details: THE STRUCTURE WAS REFINED INITIALLY WITH X-PLOR TO A RESIDUAL OF 0.203 (25509 REFLECTIONS) AND A FREE R OF 0.224 (2830 REFLECTIONS). PROFFT (FINZEL), MODIFIED TO INCORPORATE A TWO LINE ...Details: THE STRUCTURE WAS REFINED INITIALLY WITH X-PLOR TO A RESIDUAL OF 0.203 (25509 REFLECTIONS) AND A FREE R OF 0.224 (2830 REFLECTIONS). PROFFT (FINZEL), MODIFIED TO INCORPORATE A TWO LINE WEIGHTING SCHEME (SMITH), WAS USED TO PERFORM THE FINAL REFINEMENTS INCLUDING CONTRIBUTIONS FROM HYDROGEN ATOMS. DISORDERED RESIDUES WERE IDENTIFIED GRAPHICALLY.
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Displacement parameters | Biso mean: 10.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.163 / Rfactor obs: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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