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- PDB-1ff4: X-RAY STRUCTURE OF MUSCARINIC TOXIN 2 AT 1.5 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ff4
TitleX-RAY STRUCTURE OF MUSCARINIC TOXIN 2 AT 1.5 ANGSTROM RESOLUTION
ComponentsMUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN
KeywordsTOXIN / three fingers motif
Function / homology
Function and homology information


: / toxin activity / extracellular region
Similarity search - Function
Snake toxin/toxin-like / Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsMenez, R. / Le Du, M.H. / Gaucher, J.F. / Menez, A.
CitationJournal: To be Published
Title: X-ray structure of muscarinic toxin 2 at 1.5 Angstrom resolution
Authors: Menez, R. / Le Du, M.H. / Gaucher, J.F. / Menez, A.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1892
Polymers7,0931
Non-polymers961
Water1,38777
1
A: MUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN
hetero molecules

A: MUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3784
Polymers14,1862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
2
A: MUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN
hetero molecules

A: MUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3784
Polymers14,1862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area1690 Å2
ΔGint-42 kcal/mol
Surface area7160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.000, 63.000, 37.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer constructed by crystallographic two-fold symmetry

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Components

#1: Protein MUSCARINIC TOXIN/ACETYLCHOLINE RECEPTOR BINDING PROTEIN / MUSCARINIC THREE-FINGERS TOXIN


Mass: 7093.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dendroaspis angusticeps (eastern green mamba)
Secretion: VENOM / References: UniProt: P18328
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: Ammonium Sulfate, Tampon sodium acetate, pH 4.5, VAPOR DIFFUSION, temperature 20K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 13168 / Num. obs: 108000 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.488 / % possible all: 93.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 1.5→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: xplor / Details: used simulated annealing procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.244 642 -random
Rwork0.205 ---
all0.21 12710 --
obs0.21 13168 5 %-
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms490 0 5 77 572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.595
X-RAY DIFFRACTIONx_torsion_impr_deg1.493

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