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- PDB-1fsc: Crystal Structure of Fasciculin 2 from Green Mamba Snake Venom: E... -

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Basic information

Entry
Database: PDB / ID: 1fsc
TitleCrystal Structure of Fasciculin 2 from Green Mamba Snake Venom: Evidence for Unusual Loop Flexibility
ComponentsFASCICULIN 2
KeywordsSNAKE TOXIN
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Fasciculin-1 / Fasciculin-2
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHousset, 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
DepositionMar 27, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET SHEET_ID: AB, DETERMINATION METHOD: DSSP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FASCICULIN 2


Theoretical massNumber of molelcules
Total (without water)6,7693
Polymers6,7691
Non-polymers02
Water99155
1
A: FASCICULIN 2

A: FASCICULIN 2


Theoretical massNumber of molelcules
Total (without water)13,5386
Polymers13,5382
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)48.930, 48.930, 82.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO 31 / 2: CIS PROLINE - PRO 56

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Components

#1: Protein FASCICULIN 2


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
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTURN DETERMINATION METHOD: DSSP
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal
*PLUS
Density % sol: 66 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.05 Mammonium acetate1drop
335 %satammonium sulfate1reservoir
45 mMbeta-octylglucoside1reservoir
50.1 MMES1reservoir

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength
11.54
SYNCHROTRONLURE DW3220.9
Detector
TypeIDDetectorDate
XENTRONICS1AREA DETECTOR1992
MARRESEARCH2IMAGE PLATE1992
RadiationScattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.91
ReflectionNum. 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

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
RefinementResolution: 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.
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 6287 88 %
Displacement parametersBiso mean: 27.82 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms464 0 2 55 521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.93
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.93
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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