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- PDB-2etf: Crystal structure of full length botulinum neurotoxin (Type B) li... -

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Basic information

Entry
Database: PDB / ID: 2etf
TitleCrystal structure of full length botulinum neurotoxin (Type B) light chain
ComponentsBotulinum neurotoxin B light chain
KeywordsHYDROLASE / BOTULINUM / METALLOPROTEASE / CATALYTIC / 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 / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSwaminathan, S. / Eswaramoorthy, S.
CitationJournal: To be Published
Title: Crystal structure of full length botulinum neurotoxin (Type B) light chain
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Non-polymer description
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin B light chain
B: Botulinum neurotoxin B light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6478
Polymers102,1322
Non-polymers5156
Water5,999333
1
A: Botulinum neurotoxin B light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2283
Polymers51,0661
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Botulinum neurotoxin B light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4205
Polymers51,0661
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.330, 101.940, 104.320
Angle α, β, γ (deg.)90.00, 129.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Botulinum neurotoxin B light chain


Mass: 51066.152 Da / Num. of mol.: 2 / Fragment: Catalytic Domain (residues 0-440)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.2
Details: Ammonium sulphate, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 48498 / Num. obs: 48498 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.149 / Num. unique all: 3559 / % possible all: 70.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EPW

1epw


Resolution: 2.29→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The missing atoms in remark 470 are due to lack of electron density for the side chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1899 -RANDOM
Rwork0.2238 ---
all-47356 --
obs-47356 93.5 %-
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7033 0 22 333 7388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0132
X-RAY DIFFRACTIONc_angle_deg1.61

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