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- PDB-1f82: BOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1f82
TitleBOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN
ComponentsBOTULINUM NEUROTOXIN TYPE B
KeywordsTOXIN / HYDROLASE / Zinc dependent protease / Botulinum neurotoxin
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 / zinc ion binding / extracellular region / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type B
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsHanson, M.A. / Stevens, R.C.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0 A resolution.
Authors: Hanson, M.A. / Stevens, R.C.
History
DepositionJun 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOTULINUM NEUROTOXIN TYPE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0762
Polymers49,0111
Non-polymers651
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.807, 62.684, 130.278
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 B


Mass: 49010.617 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Plasmid: PBN13 / Production host: Escherichia coli (E. coli) / References: UniProt: P10844, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Hepes, Polyethylene glycol MW 4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
215-25 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.785
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.785 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 107054 / Num. obs: 103629 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.464 / Num. unique all: 1986 / % possible all: 96.2
Reflection
*PLUS
Num. obs: 30913 / Num. measured all: 107054
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2.2→15.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1108080.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Leonard-Jones
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1124 5 %RANDOM
Rwork0.244 ---
all0.244 30913 --
obs0.228 22417 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.59 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2---0.61 Å20 Å2
3----2.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→15.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 1 238 3705
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 177 5.1 %
Rwork0.294 3273 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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