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- PDB-4hev: Clostridium Botulinum Serotype A Light Chain Inhibited By Adamant... -

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Basic information

Entry
Database: PDB / ID: 4hev
TitleClostridium Botulinum Serotype A Light Chain Inhibited By Adamantane Hydroxamate
ComponentsBotulinum neurotoxin type A light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Zn2+-dependent metalloprotease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell junction / 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 junction / 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
Chem-AXM / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSilvaggi, N.R. / Allen, K.N.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies.
Authors: Silhar, P. / Silvaggi, N.R. / Pellett, S. / Johnson, E.A. / Allen, K.N. / Janda, K.D.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 20, 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,7536
Polymers101,2042
Non-polymers5494
Water2,756153
1
A: Botulinum neurotoxin type A light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8773
Polymers50,6021
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type A light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8773
Polymers50,6021
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.601, 67.632, 99.408
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 50602.047 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Plasmid: pET15-LC425 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, 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-AXM / N-hydroxy-2-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]acetamide / Adamantane acetic acid hydroxamate


Mass: 209.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-12mg/ml enzyme in 50mM NaPO4, 2mM EDTA, pH 6.5; and 10-15% polyethylene glycol (PEG) 2,000 monomethyl ester, 0.2-0.3M K2HPO4, 0.1M D,L-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 18, 2008
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.5→40.47 Å / Num. all: 32607 / Num. obs: 31857 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 43.51 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3218 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BON

3bon


Resolution: 2.5→40.469 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic/TLS / σ(F): 1.42 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1514 4.96 %Random
Rwork0.2021 ---
all0.20657 32607 --
obs0.2044 30530 93.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→40.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 32 153 6583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026574
X-RAY DIFFRACTIONf_angle_d0.5498883
X-RAY DIFFRACTIONf_dihedral_angle_d11.8152435
X-RAY DIFFRACTIONf_chiral_restr0.042972
X-RAY DIFFRACTIONf_plane_restr0.0021137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.5810.32431180.24692249X-RAY DIFFRACTION80
2.581-2.67320.29711240.23252432X-RAY DIFFRACTION87
2.6732-2.78020.30181280.24092533X-RAY DIFFRACTION90
2.7802-2.90670.33441360.24752612X-RAY DIFFRACTION93
2.9067-3.05990.31091390.23012674X-RAY DIFFRACTION95
3.0599-3.25150.29261380.23182694X-RAY DIFFRACTION96
3.2515-3.50250.25861470.21622744X-RAY DIFFRACTION97
3.5025-3.85470.27981430.22222710X-RAY DIFFRACTION96
3.8547-4.41190.20741420.17262724X-RAY DIFFRACTION96
4.4119-5.55620.18511490.15962814X-RAY DIFFRACTION99
5.5562-40.47460.2121500.18712830X-RAY DIFFRACTION97
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)
11.1160.31550.71091.15460.2480.57980.52530.1772-0.93940.4014-0.0783-0.47610.46770.35130.87390.4465-0.0458-0.17110.11080.21740.411213.4824-5.037430.6064
20.97380.32920.64251.1902-0.23371.20110.1564-0.199-0.30980.3403-0.07650.53460.1104-0.42410.40480.2607-0.03140.07010.31230.04580.3469-2.03484.996727.5879
31.30610.38130.67740.9456-0.11121.48080.05610.0942-0.30930.1525-0.07420.16540.08330.0033-00.31540.0173-0.02030.298-0.01710.38744.12744.766418.5526
40.8996-0.61940.15511.1595-0.83480.6947-0.07850.05310.24910.47920.00640.0994-0.45950.06560.00040.5278-0.0514-0.01370.288-0.03250.240520.665732.080526.2877
51.2313-0.16360.15531.66630.13870.5946-0.02530.07150.13640.2987-0.1366-0.3701-0.28930.23580.00020.3483-0.086-0.0780.37430.04550.377631.074123.962223.704
60.6159-0.2477-0.11971.3080.69960.42120.05080.0733-0.10560.1987-0.008-0.57470.1080.32730.01350.3270.0355-0.01330.56470.06990.568739.427810.325821.3452
70.72080.35270.44760.719-0.10630.57880.08310.35220.2098-0.3874-0.1758-0.0509-0.18990.1348-0.00880.38450.03190.07250.44710.05290.303622.300327.13535.9605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 299 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 417 )
4X-RAY DIFFRACTION4chain 'B' and (resid -9 through 100 )
5X-RAY DIFFRACTION5chain 'B' and (resid 101 through 232 )
6X-RAY DIFFRACTION6chain 'B' and (resid 233 through 334 )
7X-RAY DIFFRACTION7chain 'B' and (resid 335 through 416 )

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