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- PDB-5bqn: Crystal structure of the LHn fragment of botulinum neurotoxin typ... -

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Basic information

Entry
Database: PDB / ID: 5bqn
TitleCrystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q
ComponentsBotulinum neurotoxin type D,Botulinum neurotoxin type D
KeywordsHYDROLASE / botulinum neurotoxin / targeted secretion inhibitors / endopeptidase / type D / protein engineering
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 / extracellular region / zinc ion binding
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease ...Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type D
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMasuyer, G. / Davies, J.R. / Moore, K. / Chaddock, J.A. / Acharya, K.R.
CitationJournal: Sci Rep / Year: 2015
Title: Structural analysis of Clostridium botulinum neurotoxin type D as a platform for the development of targeted secretion inhibitors.
Authors: Masuyer, G. / Davies, J.R. / Moore, K. / Chaddock, J.A. / Ravi Acharya, K.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type D,Botulinum neurotoxin type D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0942
Polymers101,8561
Non-polymers2381
Water3,549197
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint2 kcal/mol
Surface area36500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.545, 173.545, 222.191
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Botulinum neurotoxin type D,Botulinum neurotoxin type D / BoNT/D / Bontoxilysin-D


Mass: 101855.594 Da / Num. of mol.: 1
Mutation: H233Y, E230Q,H233Y, E230Q,H233Y, E230Q,H233Y, E230Q
Source method: isolated from a genetically manipulated source
Details: Engineered fragment of the botulinum neurotoxin type D with inactive catalytic domain and translocation domain. An engineered linker region is present between the two domains. Residues 442- ...Details: Engineered fragment of the botulinum neurotoxin type D with inactive catalytic domain and translocation domain. An engineered linker region is present between the two domains. Residues 442-457, 494-510, 872-884 were disordered.
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19321, bontoxilysin
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.6 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 % v/v pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M HEPES 7.5, 6 % w/v polyvinylpyrrolidone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→150 Å / Num. all: 86306 / Num. obs: 86306 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 0.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FPQ

2fpq


Resolution: 2.3→150 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 22.239 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 4277 5 %RANDOM
Rwork0.22015 ---
obs0.22144 82020 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.043 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→150 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 15 197 6902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026873
X-RAY DIFFRACTIONr_bond_other_d0.0020.026437
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9589341
X-RAY DIFFRACTIONr_angle_other_deg0.975314835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0855839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7525.505327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.657151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6341522
X-RAY DIFFRACTIONr_chiral_restr0.1090.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021568
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6025.7563356
X-RAY DIFFRACTIONr_mcbond_other2.5935.7553355
X-RAY DIFFRACTIONr_mcangle_it4.348.6214192
X-RAY DIFFRACTIONr_mcangle_other4.3398.6234193
X-RAY DIFFRACTIONr_scbond_it2.6665.8913517
X-RAY DIFFRACTIONr_scbond_other2.6655.8913517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5138.7445149
X-RAY DIFFRACTIONr_long_range_B_refined7.19944.4537657
X-RAY DIFFRACTIONr_long_range_B_other7.18544.4567619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 316 -
Rwork0.372 5899 -
obs--97.28 %
Refinement TLS params.Method: refined / Origin x: 155.925 Å / Origin y: -71.2073 Å / Origin z: 13.342 Å
111213212223313233
T0.0759 Å20.0024 Å20.0387 Å2-0.2936 Å20.0012 Å2--0.0668 Å2
L0.5321 °2-0.0494 °2-0.6803 °2-0.0105 °20.0521 °2--0.8972 °2
S-0.0615 Å °0.0754 Å °-0.0417 Å °0.0238 Å °-0.0095 Å °0.0057 Å °0.0548 Å °-0.0836 Å °0.0709 Å °

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