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- PDB-3obt: Crystal structure of Botulinum neurotoxin serotype D ligand bindi... -

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Basic information

Entry
Database: PDB / ID: 3obt
TitleCrystal structure of Botulinum neurotoxin serotype D ligand binding domain in complex with N-Acetylneuraminic acid
ComponentsBotulinum neurotoxin type D
KeywordsHYDROLASE / neurotoxin / gangalioside
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
N-acetyl-beta-neuraminic acid / Botulinum neurotoxin type D
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, K.K. / Zong, Y. / Jin, R.
CitationJournal: Biochem.J. / Year: 2010
Title: Botulinum neurotoxin serotype D attacks neurons via two carbohydrate-binding sites in a ganglioside-dependent manner.
Authors: Strotmeier, J. / Lee, K. / Volker, A.K. / Mahrhold, S. / Zong, Y. / Zeiser, J. / Zhou, J. / Pich, A. / Bigalke, H. / Binz, T. / Rummel, A. / Jin, R.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,64313
Polymers50,3211
Non-polymers1,32212
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.232, 90.044, 93.518
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: 50320.652 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botD / Production host: Escherichia coli (E. coli) / References: UniProt: P19321, bontoxilysin
#2: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / BETA-SIALIC ACID / N-Acetylneuraminic acid


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 7% PEG 10000, 0.1 M Hepes, pH 8.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.997
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2→64.86 Å / Num. all: 36111 / Num. obs: 34615 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.296 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.076.20.52632991.412195.2
2.07-2.156.70.46433341.47195.6
2.15-2.256.70.36733361.542195.9
2.25-2.376.80.27933631.505196.5
2.37-2.526.80.22434381.533198.2
2.52-2.7170.16534821.456199.1
2.71-2.997.10.10934891.318199.5
2.99-3.427.30.0635391.144199.7
3.42-4.317.30.03335840.899199.7
4.31-5070.02637510.838199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.467 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 1736 5 %RANDOM
Rwork0.1715 ---
obs0.1739 34444 97.51 %-
all-36181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.99 Å2 / Biso mean: 33.0167 Å2 / Biso min: 13.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--0.55 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 87 317 3778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223527
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.964763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8175411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07125.291172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35615620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0681513
X-RAY DIFFRACTIONr_chiral_restr0.1660.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022606
X-RAY DIFFRACTIONr_mcbond_it1.5151.52053
X-RAY DIFFRACTIONr_mcangle_it2.69323350
X-RAY DIFFRACTIONr_scbond_it3.74131474
X-RAY DIFFRACTIONr_scangle_it5.8274.51412
LS refinement shellResolution: 2→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 125 -
Rwork0.217 2263 -
all-2388 -
obs--93.06 %

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