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- PDB-3fev: Crystal structure of the chimeric muscarinic toxin MT7 with loop ... -

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Basic information

Entry
Database: PDB / ID: 3fev
TitleCrystal structure of the chimeric muscarinic toxin MT7 with loop 1 from MT1.
ComponentsFusion of Muscarinic toxin 1, Muscarinic m1-toxin1
KeywordsTOXIN / CHIMERA / ACETYLCHOLINE RECEPTOR INHIBITOR / GREEN MAMBA SNAKE TOXIN / HM1 MUSCARINIC RECEPTOR / NEUROTOXIN / MUSCARINIC TOXIN / POSTSYNAPTIC NEUROTOXIN / Secreted
Function / homology
Function and homology information


receptor antagonist activity / 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
Muscarinic toxin 1 / Muscarinic toxin 7
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsStura, E.A. / Menez, R. / Mourier, G. / Fruchart-Gaillard, C. / Menez, A. / Servant, D.
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
DepositionDec 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1
B: Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1
C: Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3225
Polymers22,1293
Non-polymers1922
Water9,260514
1
A: Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1


Theoretical massNumber of molelcules
Total (without water)7,3761
Polymers7,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4732
Polymers7,3761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4732
Polymers7,3761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.140, 71.975, 89.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion of Muscarinic toxin 1, Muscarinic m1-toxin1 / MTx1 / MT1 / m1-toxin / Muscarinic toxin 7 / MT-7 / MT7


Mass: 7376.481 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in toxins MT1 and MT7
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: P81030, UniProt: Q8QGR0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHIMERIC MT1-MT7 TOXIN, FUSION OF MT1 (UNIPROT RESIDUES 1-16) AND MT7 (UNIPROT RESIDUES 38-86)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50mM sodium acetate, 0.02% NaN3, 1M ammonium sulfate, 90mM sodium citrate, 8% 1,6 hexanediol, 6% propanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2005 / Details: mirrors
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.3→28.04 Å / Num. all: 44204 / Num. obs: 39130 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 10.675 Å2 / Rmerge(I) obs: 0.155 / Rsym value: 0.156 / Net I/σ(I): 3
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3729 / Rsym value: 0.65 / % possible all: 71.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VLW

2vlw


Resolution: 1.3→28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.126 / SU ML: 0.049 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23322 2063 5 %RANDOM
Rwork0.21466 ---
all0.2156 38919 --
obs0.2156 38919 92.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.626 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 10 514 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221731
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9552360
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8145218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11923.46278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7351514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021335
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.2929
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21179
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2467
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2154
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.2169
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9481.51085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2421735
X-RAY DIFFRACTIONr_scbond_it1.9883736
X-RAY DIFFRACTIONr_scangle_it2.8264.5625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.295→1.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 127 -
Rwork0.343 2471 -
obs--80.81 %

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