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- PDB-3n7k: Crystal structure of botulinum neurotoxin serotype C1 binding domain -

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Basic information

Entry
Database: PDB / ID: 3n7k
TitleCrystal structure of botulinum neurotoxin serotype C1 binding domain
ComponentsBotulinum neurotoxin type C1
KeywordsTOXIN / botulinum neurotoxin / Ganglioside GD1b / HCR/C / Ganglioside binding loop
Function / homology
Function and homology information


symbiont-mediated suppression of host neurotransmitter secretion / ganglioside binding / Toxicity of botulinum toxin type C (botC) / membrane protein proteolysis / negative regulation of calcium ion-dependent exocytosis / bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / 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 C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFu, Z. / Kroken, A. / Karalewitz, 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 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type C1
B: Botulinum neurotoxin type C1


Theoretical massNumber of molelcules
Total (without water)99,0702
Polymers99,0702
Non-polymers00
Water1,982110
1
A: Botulinum neurotoxin type C1


Theoretical massNumber of molelcules
Total (without water)49,5351
Polymers49,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type C1


Theoretical massNumber of molelcules
Total (without water)49,5351
Polymers49,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.180, 77.350, 107.390
Angle α, β, γ (deg.)90.00, 116.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Botulinum neurotoxin type C1 / BoNT/C1 / Bontoxilysin-C1 / Botulinum neurotoxin C1 heavy chain


Mass: 49535.188 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain (UNP Residues 866-1291)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: clostridium phage c-st gene / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P18640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES buffer pH 6.5, 12% PEG 20000, 0.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 2008 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -H,-K,H+L / Fraction: 0.113
ReflectionResolution: 2.5→29.84 Å / Num. obs: 45896 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.105 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.9 / % possible all: 67.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CCP4model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N7J

3n7j


Resolution: 2.5→29.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 139023.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED Twin Details Number of Twin Domain: 2 Twin Domain: 1 Twin operator: H, K, L Twin Fraction: 0.887 Twin Dimain: 2 Twin Operator: -H, -K, H+L Twin Fraction: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2085 4.6 %RANDOM
Rwork0.223 ---
obs0.223 45820 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.9955 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-2.2 Å2
2--3.72 Å20 Å2
3----4.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6925 0 0 110 7035
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.402 136 3.5 %
Rwork0.349 3751 -
obs--78.4 %
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

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