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- PDB-2xhl: Structure of a functional derivative of Clostridium botulinum neu... -

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Basic information

Entry
Database: PDB / ID: 2xhl
TitleStructure of a functional derivative of Clostridium botulinum neurotoxin type B
Components
  • BOTULINUM NEUROTOXIN B HEAVY CHAIN
  • BOTULINUM NEUROTOXIN B LIGHT CHAIN
KeywordsHYDROLASE / METALLOPROTEASE / MEMBRANE DOMAIN / ENDOPEPTIDASE / ZINC PROTEASE / BOTULISM / TOXIN
Function / homology
Function and homology information


Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
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 B
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMasuyer, G. / Beard, M. / Cadd, V.A. / Chaddock, J.A. / Acharya, K.R.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structure and Activity of a Functional Derivative of Clostridium Botulinum Neurotoxin B.
Authors: Masuyer, G. / Beard, M. / Cadd, V.A. / Chaddock, J.A. / Acharya, K.R.
History
DepositionJun 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jan 31, 2024Group: Atomic model / Category: atom_site / Item: _atom_site.pdbx_formal_charge
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOTULINUM NEUROTOXIN B LIGHT CHAIN
B: BOTULINUM NEUROTOXIN B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1163
Polymers102,0512
Non-polymers651
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-82.2 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.890, 149.100, 113.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BOTULINUM NEUROTOXIN B LIGHT CHAIN / BONT/B / BONTOXILYSIN-B


Mass: 52291.562 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: MODIFIED PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10844, bontoxilysin
#2: Protein BOTULINUM NEUROTOXIN B HEAVY CHAIN / BONT/B / BONTOXILYSIN-B


Mass: 49759.141 Da / Num. of mol.: 1 / Fragment: RESIDUES 446-858
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: MODIFIED PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10844
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsOWING TO THE PRESENCE OF AN INTERNAL EXPRESSION TAG FOR CLEAVAGE BETWEEN THE TWO CHAINS THE ...OWING TO THE PRESENCE OF AN INTERNAL EXPRESSION TAG FOR CLEAVAGE BETWEEN THE TWO CHAINS THE NUMBERING OF THE B-CHAIN IS ADVANCED BY FIFTEEN POSITIONS COMPARED WITH THE UNENGINEERED CASE.

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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: 2.8 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.2
Details: 15% PEG3350, 0.1M BIS-TRIS-PROPANE PH 6.5, 0.2M SODIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2010 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.8→37.64 Å / Num. obs: 28644 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EPW

1epw


Resolution: 2.8→113.49 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.853 / SU B: 33.922 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 208-218,626-630 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.28231 1448 5.1 %RANDOM
Rwork0.23999 ---
obs0.24213 27162 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.557 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å20 Å20 Å2
2--0.48 Å20 Å2
3---2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.8→113.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6828 0 1 31 6860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226968
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8551.9649422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3715836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81725.903349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.921151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9141518
X-RAY DIFFRACTIONr_chiral_restr0.0580.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215261
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3041.54190
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5726828
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.55832778
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0174.52594
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 102 -
Rwork0.276 1966 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64570.2305-0.180.69160.24530.92880.0493-0.06130.1295-0.0182-0.1130.053-0.03760.01340.06380.03920.0079-0.03240.0366-0.01370.090233.644730.832118.6171
20.33870.11840.0790.3440.18880.49070.0159-0.12510.06580.0622-0.10940.0960.0894-0.06950.09360.0381-0.00370.01710.0985-0.0820.089316.19713.203334.7492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 441
2X-RAY DIFFRACTION2B458 - 872

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