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- PDB-3bon: Structure of the C. botulinum neurotoxin serotype A with Zn2+ cof... -

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Basic information

Entry
Database: PDB / ID: 3bon
TitleStructure of the C. botulinum neurotoxin serotype A with Zn2+ cofactor bound
ComponentsNeurotoxin A
KeywordsTOXIN / botulinum / neurotoxin / metalloprotease
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / 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
Bont/A1 / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsSilvaggi, N.R. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2008
Title: Catalytic features of the botulinum neurotoxin A light chain revealed by high resolution structure of an inhibitory peptide complex.
Authors: Silvaggi, N.R. / Wilson, D. / Tzipori, S. / Allen, K.N.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: Neurotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8592
Polymers48,7931
Non-polymers651
Water12,142674
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.500, 66.600, 65.400
Angle α, β, γ (deg.)90.000, 99.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neurotoxin A


Mass: 48793.094 Da / Num. of mol.: 1 / Fragment: LIGHT-CHAIN (residues 1-425)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: BOTA, ATX, BNA / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: A2I2U2, UniProt: P0DPI1*PLUS
#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.: 674 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 20% PEG 3350, 0.1M AMMONIUM TARTRATE, pH 6.9, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2007
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 131111 / Num. obs: 125605 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.048 / Χ2: 0.838 / Net I/σ(I): 21
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.9 / Num. unique all: 11383 / Χ2: 0.69 / % possible all: 87

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
RefinementStarting model: PDB ID 3BOK

3bok


Resolution: 1.2→19.691 Å / FOM work R set: 0.928 / σ(F): 0 / Stereochemistry target values: ML / Details: Riding hydrogen atoms were used in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.16 6333 5.05 %RANDOM
Rwork0.132 ---
all0.132 125580 --
obs0.133 125605 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.809 Å2 / ksol: 0.466 e/Å3
Displacement parametersBiso max: 55.85 Å2 / Biso mean: 15.75 Å2 / Biso min: 1.39 Å2
Baniso -1Baniso -2Baniso -3
1-5.579 Å2-0 Å22.395 Å2
2---3.237 Å2-0 Å2
3----2.342 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 1 674 4170
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.0891
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_chiral_restr0.0961
X-RAY DIFFRACTIONf_dihedral_angle_d18.5041
X-RAY DIFFRACTIONf_plane_restr0.0071
X-RAY DIFFRACTIONf_nbd_refined3.7561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.2140.2031680.1643284345296.55
1.214-1.2280.2091970.163730392796.55
1.228-1.2430.1972150.1543886410196.53
1.243-1.2590.1832170.1463920413796.83
1.259-1.2750.1922260.1453896412296.89
1.275-1.2930.1771850.1353932411796.8
1.293-1.3110.1592270.1263950417797.21
1.311-1.3310.1542130.1193984419797.24
1.331-1.3520.1642090.1143927413697.29
1.352-1.3740.1612150.1143998421397.24
1.374-1.3970.1562170.113961417897.71
1.397-1.4230.1562250.1033978420397.75
1.423-1.450.1432150.1034008422397.68
1.45-1.480.1382260.0963983420997.7
1.48-1.5120.1211850.0964024420997.73
1.512-1.5470.1282110.0954025423698.22
1.547-1.5860.1412140.0913995420998.18
1.586-1.6280.1372330.0894025425898.42
1.628-1.6760.132300.094017424798.01
1.676-1.730.1312040.094058426298.77
1.73-1.7920.1422250.0974034425998.38
1.792-1.8640.1392070.1014071427899.07
1.864-1.9490.1221710.1094097426898.86
1.949-2.0510.1452470.1094080432798.94
2.051-2.180.1462080.1144101430999.1
2.18-2.3480.1432150.1184119433499.07
2.348-2.5840.1512060.1354116432299.05
2.584-2.9560.1922160.1464134435097.84
2.956-3.7210.1552070.1514036424392.58
3.721-19.6940.1761990.1653630382982.98

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