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

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Basic information

Entry
Database: PDB / ID: 3neq
TitleCrystal structure of the chimeric muscarinic toxin MT7 with loop 3 from MT1
ComponentsThree-finger muscarinic toxin 7
KeywordsTOXIN / Chimeric muscarinic toxin / hM1-muscarinic receptor / snake toxin / green mamba
Function / homology
Function and homology information


receptor antagonist activity / 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 / 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: 1.25 Å
AuthorsStura, E.A. / Servent, D. / Menez, R. / Mournier, G. / Menez, A. / Fruchart-Gaillard, C.
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
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jul 4, 2012Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Three-finger muscarinic toxin 7
B: Three-finger muscarinic toxin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5786
Polymers15,1932
Non-polymers3844
Water5,495305
1
A: Three-finger muscarinic toxin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7893
Polymers7,5971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Three-finger muscarinic toxin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7893
Polymers7,5971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Three-finger muscarinic toxin 7
hetero molecules

A: Three-finger muscarinic toxin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5786
Polymers15,1932
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546x+1/2,-y-1/2,-z+11
Buried area1370 Å2
ΔGint-50 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.820, 56.578, 80.709
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 Three-finger muscarinic toxin 7 / MT7 / Muscarinic m1-toxin 1 / MTx1 / MT7 / Muscarinic m1-toxin 1


Mass: 7596.732 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Sequence from two muscarinic toxins with different selectivity for hM1
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: Q8QGR0, UniProt: P81030
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: Crystallization by evaporation using a screw cap eppendorf tube and allowing slow leaking through the rubber seal. Crystal stabilization is 1M ammonium sulfate, 5% methyl pentane diol before ...Details: Crystallization by evaporation using a screw cap eppendorf tube and allowing slow leaking through the rubber seal. Crystal stabilization is 1M ammonium sulfate, 5% methyl pentane diol before transfering to 80% saturated lithium sulfate as cryosalt and flash cooling in liquid ethane. pH 5.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975598 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2005 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975598 Å / Relative weight: 1
ReflectionResolution: 1.25→40.355 Å / Num. obs: 33683 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.145 / Rsym value: 0.039 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.25-1.3213.40.953.90.2591100
3.95-56.5812.60.09121.30.028199.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VLW

2vlw


Resolution: 1.25→32.854 Å / Occupancy max: 1 / Occupancy min: 0.07 / SU ML: 0.14 / Isotropic thermal model: Anisotropic / σ(F): 1.47 / Phase error: 12.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1678 1703 5.07 %
Rwork0.1473 --
obs0.1483 33614 99.98 %
all-35317 -
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.825 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→32.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 20 305 1377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071335
X-RAY DIFFRACTIONf_angle_d1.2171833
X-RAY DIFFRACTIONf_dihedral_angle_d13.948527
X-RAY DIFFRACTIONf_chiral_restr0.087189
X-RAY DIFFRACTIONf_plane_restr0.006244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28680.22671370.20822626X-RAY DIFFRACTION100
1.2868-1.32830.19321370.17672576X-RAY DIFFRACTION100
1.3283-1.37580.16611270.15092660X-RAY DIFFRACTION100
1.3758-1.43090.15851470.12852631X-RAY DIFFRACTION100
1.4309-1.4960.15611390.11022595X-RAY DIFFRACTION100
1.496-1.57490.12661470.1082627X-RAY DIFFRACTION100
1.5749-1.67360.11981620.10422620X-RAY DIFFRACTION100
1.6736-1.80280.15471300.11272661X-RAY DIFFRACTION100
1.8028-1.98420.171410.14112673X-RAY DIFFRACTION100
1.9842-2.27120.16371280.14482693X-RAY DIFFRACTION100
2.2712-2.86120.18331700.16322693X-RAY DIFFRACTION100
2.8612-32.86520.17741380.16492856X-RAY DIFFRACTION100

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