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- PDB-7uls: Recombinant muscarinic toxin alpha -

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Basic information

Entry
Database: PDB / ID: 7uls
TitleRecombinant muscarinic toxin alpha
ComponentsMuscarinic toxin alpha
KeywordsBIOSYNTHETIC PROTEIN / recombinant / muscarinic toxin / refolded
Function / homologySnake toxin/toxin-like / Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Snake toxin-like superfamily / toxin activity / extracellular region / Muscarinic toxin alpha
Function and homology information
Biological speciesDendroaspis polylepis polylepis (black mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, J. / Lei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM064642 United States
CitationJournal: To Be Published
Title: recombinant MTalpha at 1.8 Angstroms resolution
Authors: Xu, J. / Lei, X. / Chen, L.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscarinic toxin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8783
Polymers7,6941
Non-polymers1842
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.555, 58.555, 35.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Muscarinic toxin alpha / MT-alpha


Mass: 7693.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis polylepis polylepis (black mamba)
Production host: Escherichia coli (E. coli) / References: UniProt: P80494
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 128 mg/ml in 200 mM NH4Ac (pH 7.0), 1:1(v/v) with 1.26 M sodium phosphate monobasic monohydrate, 0.14 M potassium phosphate, pH 5.6 at 18 degree centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00007 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00007 Å / Relative weight: 1
ReflectionResolution: 1.5→29.28 Å / Num. obs: 11189 / % possible obs: 99.4 % / Redundancy: 9.3 % / Biso Wilson estimate: 21.26 Å2 / Rpim(I) all: 0.017 / Rrim(I) all: 0.052 / Net I/σ(I): 53.4
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.494 / Num. unique obs: 523

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DO8

4do8


Resolution: 1.8→29.28 Å / SU ML: 0.0609 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 30.8048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2199 336 5.15 %
Rwork0.1895 6192 -
obs0.1911 6528 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms532 0 12 69 613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069555
X-RAY DIFFRACTIONf_angle_d0.9079750
X-RAY DIFFRACTIONf_chiral_restr0.042582
X-RAY DIFFRACTIONf_plane_restr0.005793
X-RAY DIFFRACTIONf_dihedral_angle_d11.4702200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-2.270.28171520.25453076X-RAY DIFFRACTION99.91
2.27-29.280.2021840.16683116X-RAY DIFFRACTION99.88

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