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- PDB-4do8: Crystal structure of the muscarinic toxin MT1 -

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Basic information

Entry
Database: PDB / ID: 4do8
TitleCrystal structure of the muscarinic toxin MT1
ComponentsMuscarinic toxin 1
KeywordsTOXIN / snake toxin / Three-finger toxin fold / Muscarinic toxin / MUSCARINIC M1 receptor / neurones / MUSCARINIC M4 receptor / adrenergic receptor
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / THIOCYANATE ION / Muscarinic toxin 1
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsFruchart-Gaillard, C. / Mournier, G. / Vera, L. / Servent, D. / Stura, E.A.
CitationJournal: Plos One / Year: 2012
Title: Engineering of three-finger fold toxins creates ligands with original pharmacological profiles for muscarinic and adrenergic receptors.
Authors: Fruchart-Gaillard, C. / Mourier, G. / Blanchet, G. / Vera, L. / Gilles, N. / Menez, R. / Marcon, E. / Stura, E.A. / Servent, D.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Muscarinic toxin 1
B: Muscarinic toxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1684
Polymers15,0512
Non-polymers1172
Water2,432135
1
A: Muscarinic toxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5842
Polymers7,5261
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscarinic toxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5852
Polymers7,5261
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Muscarinic toxin 1
B: Muscarinic toxin 1
hetero molecules

A: Muscarinic toxin 1
B: Muscarinic toxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3378
Polymers30,1024
Non-polymers2344
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5290 Å2
ΔGint-37 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.280, 116.040, 46.190
Angle α, β, γ (deg.)90.00, 108.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Muscarinic toxin 1 / MT1 / MTx1


Mass: 7525.621 Da / Num. of mol.: 2 / Fragment: Muscarinic toxin 1 / Source method: obtained synthetically
Details: Synthetic construct of natural toxin from Dendroaspis angusticeps.
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: P81030
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 8.3 mg/mL in 0.05M sodium Acetate pH 5.5. Precipitant: 36% MPEG 2K, 0.1mM imidazole-HCl, .45M NaCl, 0.09M KSCN, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 14956 / Num. obs: 14793 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.06 % / Biso Wilson estimate: 34.018 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.081 / Net I/σ(I): 10.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.8-1.913.960.7292.523250.63396
1.91-2.044.110.3524.9922500.30799.7
2.04-2.214.160.2147.521040.187100
2.21-2.424.160.1669.3819360.14599.8
2.42-2.74.140.10913.0417630.09599.5
2.7-3.124.070.08316.7815380.072100
3.12-3.813.980.07319.7213160.06399.5
3.81-5.373.880.06920.6810200.0699.2
5.37-503.780.06220.485410.05493.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RHO-DA1A (UNPUBLISHED)

Resolution: 1.802→35.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.806 / SU ML: 0.097 / Isotropic thermal model: Isotropic / TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.128 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23377 740 5 %RANDOM
Rwork0.19266 ---
obs0.19472 14044 100 %-
all-14793 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.789 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20.07 Å2
2---1.25 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.802→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 7 135 1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.9551502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8345134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81824.09144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10115186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.793156
X-RAY DIFFRACTIONr_chiral_restr0.1440.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021822
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4161.5679
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23421115
X-RAY DIFFRACTIONr_scbond_it3.4313421
X-RAY DIFFRACTIONr_scangle_it5.1024.5387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 51 -
Rwork0.289 971 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69920.2584-0.02183.9579-1.88392.60110.04170.0210.07810.3732-0.165-0.08660.1438-0.07810.12320.1164-0.0635-0.00850.1184-0.00820.12732.0482.98410.257
20.4482-0.7253-0.75014.55792.0342.7060.12320.01730.03470.4002-0.20310.1895-0.29660.00340.07990.1883-0.05360.02970.0695-0.00350.0998-2.08830.27910.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2B1 - 66

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