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- PDB-3n7m: Crystal structure of W1252A mutant of HCR D/C VPI 5995 -

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Basic information

Entry
Database: PDB / ID: 3n7m
TitleCrystal structure of W1252A mutant of HCR D/C VPI 5995
ComponentsNeurotoxin
KeywordsTOXIN / Botulinum neurotoxin / W1252A mutant / GM1a / Ganglioside binding loop
Function / homology
Function and homology information


protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsFu, Z. / Karalewitz, A. / Kroken, A. / Baldwin, M.R. / Barbieri, J.T. / Kim, J.-J.P.
CitationJournal: Biochemistry / Year: 2010
Title: Identification of a Unique Ganglioside Binding Loop within Botulinum Neurotoxins C and D-SA .
Authors: Karalewitz, A.P. / Kroken, A.R. / Fu, Z. / Baldwin, M.R. / Kim, J.J. / Barbieri, J.T.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Structure summary
Revision 1.3Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1113
Polymers48,9231
Non-polymers1882
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.389, 57.795, 184.664
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 Neurotoxin /


Mass: 48923.039 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain (UNP residues 862-1285) / Mutation: W1252A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: Clostridium Neurotoxin / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: Q9LBR1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 4% PEG400, 45% ammonium sulfate, 250mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2009
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→28.55 Å / Num. obs: 19457 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.098 / Net I/σ(I): 15.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.526 / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3N7L

3n7l


Resolution: 2.6→28.55 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 88131.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 879 4.9 %RANDOM
Rwork0.222 ---
obs0.222 18101 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9334 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.5 Å20 Å20 Å2
2--0.89 Å20 Å2
3----15.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.6→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 11 56 3470
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.492.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.6→2.64 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 42 5.5 %
Rwork0.323 725 -
obs--78.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4so4.parso4.top
X-RAY DIFFRACTION5gol.pargol.top

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