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- PDB-3qix: Crystal Structure of BoNT/A LC with Zinc bound -

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Basic information

Entry
Database: PDB / ID: 3qix
TitleCrystal Structure of BoNT/A LC with Zinc bound
ComponentsBotulinum neurotoxin type A
KeywordsHYDROLASE / Botulinum / BONT / Neurotoxin / Toxin / metalloprotease / protease
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
Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9445
Polymers98,7512
Non-polymers1933
Water2,198122
1
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5033
Polymers49,3761
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4412
Polymers49,3761
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.808, 193.747, 56.003
Angle α, β, γ (deg.)90.000, 96.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 49375.664 Da / Num. of mol.: 2 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
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: ALS / Beamline: 12.3.1 / Wavelength: 1.044
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2009
RadiationMonochromator: 1: Double Crystal 2: Double Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 13.9 / Number: 118707 / Rmerge(I) obs: 0.093 / Χ2: 1 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 31317 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175099.910.03613.8
4.15.1799.810.0630.9883.8
3.584.110010.0780.9923.8
3.263.5810010.10.9873.8
3.023.2610010.1341.0013.8
2.853.0210010.1921.0063.8
2.72.8510010.2590.9973.8
2.592.710010.3251.0143.8
2.492.5910010.421.0053.8
2.42.4999.910.4780.9763.7
ReflectionResolution: 2.4→50 Å / Num. obs: 31317 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Χ2: 0.997 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.493.70.47830890.976199.9
2.49-2.593.80.4231361.0051100
2.59-2.73.80.32531201.0141100
2.7-2.853.80.25931310.9971100
2.85-3.023.80.19231151.0061100
3.02-3.263.80.13431431.0011100
3.26-3.583.80.131360.9871100
3.58-4.13.80.07831080.9921100
4.1-5.173.80.06331550.988199.8
5.17-503.80.03631841199.9

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Processing

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

3dda


Resolution: 2.413→48.437 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1489 5.06 %RANDOM
Rwork0.185 ---
obs0.1873 29450 93.56 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.386 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 128.08 Å2 / Biso mean: 44.953 Å2 / Biso min: 16.11 Å2
Baniso -1Baniso -2Baniso -3
1-6.0117 Å2-0 Å24.5944 Å2
2---1.9445 Å20 Å2
3----4.0672 Å2
Refinement stepCycle: LAST / Resolution: 2.413→48.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 6 122 6488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126527
X-RAY DIFFRACTIONf_angle_d1.4018813
X-RAY DIFFRACTIONf_chiral_restr0.091959
X-RAY DIFFRACTIONf_plane_restr0.0051135
X-RAY DIFFRACTIONf_dihedral_angle_d15.72401
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 (%)
2.4134-2.49130.27941050.22962210231581
2.4913-2.58030.31141230.22522393251687
2.5803-2.68360.28451210.21282395251689
2.6836-2.80570.30281340.21742513264792
2.8057-2.95360.26041440.20352512265693
2.9536-3.13870.29311190.19592558267795
3.1387-3.38090.23231370.18572606274396
3.3809-3.72110.211360.17722678281498
3.7211-4.25920.20911560.15822677283399
4.2592-5.36510.18181550.15492698285399
5.3651-48.44650.20911590.19827212880100
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)
10.602-0.0192-0.18250.7612-0.23090.8728-0.02160.0776-0.015-0.09270.02630.00260.1154-0.07160.01840.27620.0234-0.01480.1884-0.00630.16626.29199.893415.5183
21.34090.226-0.23631.1053-0.27361.20520.02040.07270.04870.0489-0.02230.04110.0427-0.0220.00440.11440.0134-0.00140.04950.01280.06434.543616.940824.7895
30.69190.3036-0.18481.4629-0.13461.18230.0676-0.12330.08080.3075-0.1115-0.0649-0.10170.06430.00790.1471-0.0021-0.00380.13390.0010.12278.845922.617632.1681
40.51720.02220.24121.07060.41740.7778-0.04070.1520.0728-0.1932-0.0430.0166-0.31530.0271-0.05520.32050.0440.07190.18420.06660.1766-11.235172.5676-11.0523
51.35720.21820.4931.40530.78081.38960.0630.1005-0.05110.00960.0422-0.1093-0.12120.0005-0.11090.19860.01090.05520.1448-0.00050.1311-8.967164.4985-2.1495
61.08770.37120.74512.21960.89741.62520.1563-0.0423-0.1250.4958-0.01150.00360.1962-0.2027-0.08490.2188-0.01030.05020.16210.02280.1338-13.62558.50425.256
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 269:420)A269 - 420
4X-RAY DIFFRACTION4(chain B and resid 2:70)B2 - 70
5X-RAY DIFFRACTION5(chain B and resid 71:268)B71 - 268
6X-RAY DIFFRACTION6(chain B and resid 269:419)B269 - 419

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