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- PDB-3qiy: Crystal Structure of BoNT/A LC complexed with Hydroxamate-based I... -

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Basic information

Entry
Database: PDB / ID: 3qiy
TitleCrystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-1
ComponentsBotulinum neurotoxin type A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Botulinum / BONT / Neurotoxin / Toxin / Hydroxamate / Inhibitor / metalloprotease / protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell junction / Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / membrane => GO:0016020 ...host cell junction / Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / membrane => GO:0016020 / 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 C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-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
4-[bis(4-chlorobenzyl)amino]-N-hydroxybutanamide / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsThompson, A.A. / Han, G.W. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 2011
Title: Structural Characterization of Three Novel Hydroxamate-Based Zinc Chelating Inhibitors of the Clostridium botulinum Serotype A Neurotoxin Light Chain Metalloprotease Reveals a Compact Binding ...Title: Structural Characterization of Three Novel Hydroxamate-Based Zinc Chelating Inhibitors of the Clostridium botulinum Serotype A Neurotoxin Light Chain Metalloprotease Reveals a Compact Binding Site Resulting from 60/70 Loop Flexibility.
Authors: Thompson, A.A. / Jiao, G.S. / Kim, S. / Thai, A. / Cregar-Hernandez, L. / Margosiak, S.A. / Johnson, A.T. / Han, G.W. / O'Malley, S. / Stevens, R.C.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_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_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

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9325
Polymers49,3761
Non-polymers5574
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.075, 190.594, 42.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 49375.664 Da / Num. of mol.: 1 / Fragment: light chain (UNP residues 3-424)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: Hall - Serotype A / Gene: botA, CBO0806, CLC_0862, Neurotoxin Light Chain / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: A5HZZ9, UniProt: P0DPI0*PLUS, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QI1 / 4-[bis(4-chlorobenzyl)amino]-N-hydroxybutanamide


Mass: 367.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20Cl2N2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 13% PEG6000, 100 mM MES, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2010
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 13.4 % / Av σ(I) over netI: 10.77 / Number: 274889 / Rmerge(I) obs: 0.096 / Χ2: 1 / D res high: 2.3 Å / D res low: 45 Å / Num. obs: 20556 / % possible obs: 91.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.95459510.0690.98415.7
3.934.9598.510.0860.99615.6
3.443.9389.610.0931.0110.9
3.123.4499.610.1180.98715
2.93.1299.710.1310.99415.1
2.732.997.410.1690.99314
2.592.7392.410.4241.02211.3
2.482.5992.910.2811.00511.9
2.382.4869.610.2770.98912.1
2.32.3880.710.3280.99510.5
ReflectionResolution: 2.3→45 Å / Num. obs: 20556 / % possible obs: 91.6 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.096 / Χ2: 0.996 / Net I/σ(I): 21.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3810.50.32817860.995180.7
2.38-2.4812.10.27715190.989169.6
2.48-2.5911.90.28120411.005192.9
2.59-2.7311.30.42420291.022192.4
2.73-2.9140.16921660.993197.4
2.9-3.1215.10.13122080.994199.7
3.12-3.44150.11822140.987199.6
3.44-3.9310.90.09320351.01189.6
3.93-4.9515.60.08622440.996198.5
4.95-4515.70.06923140.984195

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DDA

3dda


Resolution: 2.3→34.62 Å / Cor.coef. Fo:Fc: 0.9106 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1042 5.14 %RANDOM
Rwork0.2261 ---
obs0.228 20289 --
Displacement parametersBiso max: 218.9 Å2 / Biso mean: 88.9865 Å2 / Biso min: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-14.3663 Å20 Å20 Å2
2--22.5073 Å20 Å2
3----36.8736 Å2
Refine analyzeLuzzati coordinate error obs: 0.542 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 33 21 3226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1131SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes464HARMONIC5
X-RAY DIFFRACTIONt_it3257HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3722SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3282HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4428HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion19.43
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3029 101 4.13 %
Rwork0.2483 2347 -
all0.2503 2448 -
Refinement TLS params.Method: refined / Origin x: -16.23 Å / Origin y: 26.0612 Å / Origin z: -10.5151 Å
111213212223313233
T-0.2924 Å20.0495 Å20.0109 Å2--0.304 Å2-0.0402 Å2---0.0052 Å2
L3.9833 °2-2.3143 °20.3053 °2-5.9887 °2-0.6126 °2--1.6694 °2
S-0.0431 Å °0.274 Å °-0.0622 Å °-0.1568 Å °-0.1126 Å °-0.5442 Å °-0.2098 Å °-0.1329 Å °0.1557 Å °
Refinement TLS groupSelection details: { A|* }

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