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Yorodumi- PDB-1fsc: Crystal Structure of Fasciculin 2 from Green Mamba Snake Venom: E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fsc | ||||||
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Title | Crystal Structure of Fasciculin 2 from Green Mamba Snake Venom: Evidence for Unusual Loop Flexibility | ||||||
Components | FASCICULIN 2 | ||||||
Keywords | SNAKE TOXIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dendroaspis angusticeps (eastern green mamba) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Housset, D. / Le Du, M.H. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structure of fasciculin 2 from green mamba snake venom: evidence for unusual loop flexibility. Authors: le Du, M.H. / Housset, D. / Marchot, P. / Bougis, P.E. / Navaza, J. / Fontecilla-Camps, J.C. #1: Journal: J.Biol.Chem. / Year: 1992 Title: 1.9-Angstroms Resolution Structure of Fasciculin 1, an Anti-Acetylcholinesterase Toxin from Green Mamba Snake Venom Authors: Le Du, M.H. / Marchot, P. / Bougis, P.E. / Fontecilla-Camps, J.C. #2: Journal: J.Biol.Chem. / Year: 1989 Title: Crystals of Fasciculin 2 from Green Mamba Snake Venom Authors: Le, M.H. / Marchot, P. / Bougis, P.E. / Fontecilla-Camps, J.C. | ||||||
History |
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Remark 700 | SHEET SHEET SHEET_ID: AB, DETERMINATION METHOD: DSSP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fsc.cif.gz | 21 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fsc.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fsc_validation.pdf.gz | 364.3 KB | Display | wwPDB validaton report |
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Full document | 1fsc_full_validation.pdf.gz | 364.3 KB | Display | |
Data in XML | 1fsc_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 1fsc_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/1fsc ftp://data.pdbj.org/pub/pdb/validation_reports/fs/1fsc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 31 / 2: CIS PROLINE - PRO 56 |
-Components
#1: Protein | Mass: 6768.769 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dendroaspis angusticeps (eastern green mamba) References: UniProt: P01403, UniProt: P0C1Z0*PLUS | ||||
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#2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | Compound details | TURN DETERMINAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.12 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 66 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Num. obs: 6363 / % possible obs: 90 % / Observed criterion σ(I): 2.5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / σ(F): 2.5 Details: THE CRYSTALS ONLY GROW IN THE PRESENCE OF BETA-OCTYL GLUCOSIDE. DURING REFINEMENT THE FO-FC ELECTRON DENSITY MAP SHOWED A LARGE POSITIVE PEAK IN A HYDROPHOBIC POCKET AT THE INTERFACE BETWEEN ...Details: THE CRYSTALS ONLY GROW IN THE PRESENCE OF BETA-OCTYL GLUCOSIDE. DURING REFINEMENT THE FO-FC ELECTRON DENSITY MAP SHOWED A LARGE POSITIVE PEAK IN A HYDROPHOBIC POCKET AT THE INTERFACE BETWEEN THE TWO MOLECULES FORMING THE CRYSTALLOGRAPHIC DIMER. FOR THE PURPOSE OF REFINEMENT, TWO OXYGEN ATOMS WERE MODELED IN THIS DENSITY. VAN DER WAALS INTERACTIONS BETWEEN THESE TWO ATOMS WERE INTENTIONALLY SWITCHED OFF TO LET THEM FREE TO MOVE TO THE OPTIMAL POSITION. IT EXPLAINS THE SHORT DISTANCE (1.7 A) BETWEEN THEM. THE AUTHORS DISCUSS THIS IN THE PAPER CITED ON JRNL RECORDS AND BELIEVE THAT THIS POCKET COULD BE OCCUPIED BY PART OF THE ALIPHATIC CHAIN OF THE BETA-OCTYL GLUCOSIDE MOLECULE. THE TWO OXYGENS ARE PRESENTED AS O 156 AND O 157 BELOW.
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Displacement parameters | Biso mean: 27.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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