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- PDB-3ogg: Crystal structure of the receptor binding domain of botulinum neu... -

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Basic information

Entry
Database: PDB / ID: 3ogg
TitleCrystal structure of the receptor binding domain of botulinum neurotoxin D
ComponentsBotulinum neurotoxin type D
KeywordsTOXIN / Botulinum neurotoxin / serotype D / receptor binding domain / jelly roll trefoil fold / receptor binding / gangliosides / membrane to cytoplasm
Function / homology
Function and homology information


Toxicity of botulinum toxin type D (botD) / ganglioside GT1b binding / bontoxilysin / 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 / 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 D
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsZhang, Y. / Gao, X. / Qin, L. / Buchko, G.W. / Robinson, H. / Varnum, S.M.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Structural analysis of the receptor binding domain of botulinum neurotoxin serotype D.
Authors: Zhang, Y. / Buchko, G.W. / Qin, L. / Robinson, H. / Varnum, S.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D
Authors: Zhang, Y. / Gao, X. / Qin, L. / Buchko, G.W. / Robinson, H. / Varnum, S.M.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 D


Theoretical massNumber of molelcules
Total (without water)48,1231
Polymers48,1231
Non-polymers00
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.782, 89.680, 93.929
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 Botulinum neurotoxin type D / BoNT/D / Bontoxilysin-D / Botulinum neurotoxin D light chain / Botulinum neurotoxin D heavy chain


Mass: 48123.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botD, Botulinum Neurotoxin D / Plasmid: pJexpress / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P19321, bontoxilysin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% (w/v) PEG 4000, 0.2 M NaAC and 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→41.61 Å / Num. all: 62315 / Num. obs: 62236 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EPW

1epw


Resolution: 1.651→41.605 Å / SU ML: 0.14 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1892 3.04 %0.03
Rwork0.1725 ---
all0.1731 62315 --
obs0.1731 62236 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.27 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3131 Å20 Å2-0 Å2
2--0.6754 Å20 Å2
3----0.3623 Å2
Refinement stepCycle: LAST / Resolution: 1.651→41.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 0 508 3831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063393
X-RAY DIFFRACTIONf_angle_d1.044597
X-RAY DIFFRACTIONf_dihedral_angle_d15.4841222
X-RAY DIFFRACTIONf_chiral_restr0.083509
X-RAY DIFFRACTIONf_plane_restr0.004580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6514-1.69270.24351370.18744229X-RAY DIFFRACTION99
1.6927-1.73850.23021230.17624237X-RAY DIFFRACTION100
1.7385-1.78960.19661240.1664280X-RAY DIFFRACTION100
1.7896-1.84740.19291180.16784259X-RAY DIFFRACTION100
1.8474-1.91340.22061110.16664307X-RAY DIFFRACTION100
1.9134-1.990.20551300.1624272X-RAY DIFFRACTION100
1.99-2.08060.19671310.16134287X-RAY DIFFRACTION100
2.0806-2.19030.17731390.16034283X-RAY DIFFRACTION100
2.1903-2.32750.19791320.1664294X-RAY DIFFRACTION100
2.3275-2.50720.19271450.17164297X-RAY DIFFRACTION100
2.5072-2.75940.19811590.17794312X-RAY DIFFRACTION100
2.7594-3.15860.18751340.17184338X-RAY DIFFRACTION100
3.1586-3.9790.17281470.15714395X-RAY DIFFRACTION100
3.979-41.61790.17941620.18294554X-RAY DIFFRACTION100

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