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- PDB-2ilp: Clostridium botulinum Serotype A Light Chain inhibited by 4-chlor... -

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Basic information

Entry
Database: PDB / ID: 2ilp
TitleClostridium botulinum Serotype A Light Chain inhibited by 4-chlorocinnamic hydroxamate
ComponentsBotulinum neurotoxin A light-chain
KeywordsHYDROLASE / Clostridium botulinum neurotoxin / Type A / substrate specificity / substrate switching / protease inhibitors
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
(2E)-3-(4-CHLOROPHENYL)-N-HYDROXYACRYLAMIDE / PHOSPHATE ION / Botulinum neurotoxin type A / BoNT/A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSilvaggi, N.R. / Allen, K.N.
CitationJournal: Chem.Biol. / Year: 2007
Title: Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain Complexed with Small-Molecule Inhibitors Highlight Active-Site Flexibility.
Authors: Silvaggi, N.R. / Boldt, G.E. / Hixon, M.S. / Kennedy, J.P. / Tzipori, S. / Janda, K.D. / Allen, K.N.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 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_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_asym_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_asym_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_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 A light-chain
B: Botulinum neurotoxin A light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2567
Polymers101,6352
Non-polymers6215
Water11,079615
1
A: Botulinum neurotoxin A light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1754
Polymers50,8171
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Botulinum neurotoxin A light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0803
Polymers50,8171
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.656, 67.694, 98.396
Angle α, β, γ (deg.)90.00, 106.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere is a dimer in the asymmetric unit, but the enzyme is biologically active as a monomer.

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Components

#1: Protein Botulinum neurotoxin A light-chain


Mass: 50817.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: Serotype A / Gene: botA, atx, bna / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3)
References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GB5 / (2E)-3-(4-CHLOROPHENYL)-N-HYDROXYACRYLAMIDE / 4-CHLOROCINNAMYLHYDROXAMATE


Mass: 197.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8ClNO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10-15% PEG 2000 MMe, 0.3M (NH4)2HPO4, 0.05M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 73310 / Num. obs: 71771 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.2 / % possible all: 95.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CBASSdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.754 / SU ML: 0.091 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21556 3626 5.1 %RANDOM
Rwork0.17281 ---
obs0.17496 68126 97.86 %-
all-71771 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0.25 Å2
2--0.03 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 33 615 7294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226834
X-RAY DIFFRACTIONr_bond_other_d0.0010.024662
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9569240
X-RAY DIFFRACTIONr_angle_other_deg0.864311356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32924.586338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.029151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2651530
X-RAY DIFFRACTIONr_chiral_restr0.0760.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021451
X-RAY DIFFRACTIONr_nbd_refined0.1980.21300
X-RAY DIFFRACTIONr_nbd_other0.1840.24738
X-RAY DIFFRACTIONr_nbtor_refined0.180.23376
X-RAY DIFFRACTIONr_nbtor_other0.0830.23402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.54233
X-RAY DIFFRACTIONr_mcbond_other0.1651.51655
X-RAY DIFFRACTIONr_mcangle_it1.21226629
X-RAY DIFFRACTIONr_scbond_it1.76632997
X-RAY DIFFRACTIONr_scangle_it2.5764.52611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 240 -
Rwork0.23 4898 -
obs--95.18 %

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