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

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Basic information

Entry
Database: PDB / ID: 3qiz
TitleCrystal Structure of BoNT/A LC complexed with Hydroxamate-based Inhibitor PT-2
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 / metalloendopeptidase activity ...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 / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / 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
DI(HYDROXYETHYL)ETHER / Chem-QI2 / 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 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_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 type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9824
Polymers49,3761
Non-polymers6063
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.230, 190.654, 42.430
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-648-

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-QI2 / (2S,4R)-2-(2-{[3-(4-fluoro-3-methylphenyl)propyl](methyl)amino}ethyl)-4-(4-fluorophenyl)-N-hydroxy-4-methoxybutanamide


Mass: 434.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32F2N2O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% PEG6000, 5% glycerol, 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: 1.03
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 13, 2009
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 16.72 / Number: 207203 / Rmerge(I) obs: 0.088 / Χ2: 1 / D res high: 2 Å / D res low: 45 Å / Num. obs: 30442 / % possible obs: 90.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.314598.810.0631.0177.1
3.424.3178.210.0620.9955.9
2.993.4299.710.0960.9877.3
2.712.9999.810.1220.9837.7
2.522.7199.710.1841.0147.9
2.372.5210010.2491.0118
2.252.3779.810.3050.9927.3
2.152.2578.210.3861.0065.8
2.072.1594.210.43615.6
22.0779.710.4880.9944.6
ReflectionResolution: 2→45 Å / Num. obs: 30442 / % possible obs: 90.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.088 / Χ2: 1.001 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.074.60.48826110.994179.7
2.07-2.155.60.43630961194.2
2.15-2.255.80.38625791.006178.2
2.25-2.377.30.30526510.992179.8
2.37-2.5280.24932981.0111100
2.52-2.717.90.18433011.014199.7
2.71-2.997.70.12233150.983199.8
2.99-3.427.30.09633520.987199.7
3.42-4.315.90.06226810.995178.2
4.31-457.10.06335581.017198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DDA

3dda


Resolution: 2→37.133 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8106 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1480 5.09 %RANDOM
Rwork0.1881 ---
obs0.1899 29080 86.9 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.46 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 178.52 Å2 / Biso mean: 49.4402 Å2 / Biso min: 20.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.987 Å2-0 Å20 Å2
2---8.9778 Å2-0 Å2
3---7.9908 Å2
Refinement stepCycle: LAST / Resolution: 2→37.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 39 149 3419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013362
X-RAY DIFFRACTIONf_angle_d1.2684547
X-RAY DIFFRACTIONf_chiral_restr0.089488
X-RAY DIFFRACTIONf_plane_restr0.005587
X-RAY DIFFRACTIONf_dihedral_angle_d14.8991253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0004-2.0650.3453970.24781921201868
2.065-2.13880.26321280.23252363249183
2.1388-2.22440.28081310.23582484261588
2.2244-2.32560.3364670.28471470153752
2.3256-2.44820.26651420.21982736287896
2.4482-2.60160.30861640.22362773293797
2.6016-2.80240.2421480.21522835298398
2.8024-3.08430.24821570.20442831298899
3.0843-3.53030.22471710.19282874304599
3.5303-4.44660.20011320.15492207233976
4.4466-37.13970.16641430.15813106324999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.80481.05560.52050.92920.7870.7680.05320.0872-0.56730.0030.0158-0.43580.1720.0762-0.080.21170.01620.03760.18590.02810.3254-3.211817.9039-12.355
21.64231.65530.48262.35470.90531.5744-0.0903-0.0851-0.1109-0.1136-0.01820.0157-0.12790.02570.10620.1644-0.02270.00590.14120.01610.1597-12.409525.2118-12.6058
31.53681.30130.37643.74770.89081.30080.0827-0.33120.26960.1165-0.32530.7929-0.1891-0.16870.24070.15310.0020.00940.1432-0.03870.2494-19.359830.8435-7.6602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:69)A2 - 69
2X-RAY DIFFRACTION2(chain A and resid 70:268)A70 - 268
3X-RAY DIFFRACTION3(chain A and resid 269:421)A269 - 421

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