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- PDB-7na9: Crystal structure of BoNT/B-LC-JSG-C1 -

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Basic information

Entry
Database: PDB / ID: 7na9
TitleCrystal structure of BoNT/B-LC-JSG-C1
Components
  • Botulinum neurotoxin type B
  • JSG-C1
KeywordsTOXIN / neurotoxin / enzyme / inhibitor / antitoxin
Function / homology
Function and homology information


Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type B
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos Pathog. / Year: 2022
Title: Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies.
Authors: Lam, K.H. / Tremblay, J.M. / Perry, K. / Ichtchenko, K. / Shoemaker, C.B. / Jin, R.
History
DepositionJun 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
D: JSG-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1636
Polymers65,9122
Non-polymers2524
Water10,233568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.417, 97.018, 101.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B


Mass: 51445.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli (E. coli) / References: UniProt: P10844
#2: Antibody JSG-C1


Mass: 14466.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→101.9 Å / Num. obs: 61223 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 20.1
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 3060 / CC1/2: 0.852 / Rpim(I) all: 0.328

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.19.2_4158refinement
XDS1.18.2_3874data reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F82

1f82


Resolution: 1.76→52.6 Å / SU ML: 0.2231 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2053 3110 5.09 %
Rwork0.167 58035 -
obs0.1689 61145 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.24 Å2
Refinement stepCycle: LAST / Resolution: 1.76→52.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 13 568 5138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01634705
X-RAY DIFFRACTIONf_angle_d1.31956350
X-RAY DIFFRACTIONf_chiral_restr0.0877678
X-RAY DIFFRACTIONf_plane_restr0.0093828
X-RAY DIFFRACTIONf_dihedral_angle_d13.69531785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.38731270.31722357X-RAY DIFFRACTION90.89
1.78-1.810.32911190.27692645X-RAY DIFFRACTION99.82
1.81-1.840.2761410.23672590X-RAY DIFFRACTION100
1.84-1.880.25141440.20642621X-RAY DIFFRACTION99.96
1.88-1.910.2251400.18052638X-RAY DIFFRACTION99.96
1.91-1.950.2381240.17732616X-RAY DIFFRACTION100
1.95-20.221270.16622640X-RAY DIFFRACTION99.96
2-2.040.19891340.1652638X-RAY DIFFRACTION99.93
2.04-2.090.22041410.17152612X-RAY DIFFRACTION99.96
2.09-2.150.22371570.17752615X-RAY DIFFRACTION99.96
2.15-2.210.22171250.18092664X-RAY DIFFRACTION99.93
2.21-2.280.22621470.18772603X-RAY DIFFRACTION99.93
2.28-2.370.22571560.16822647X-RAY DIFFRACTION99.79
2.37-2.460.23161420.17432607X-RAY DIFFRACTION99.75
2.46-2.570.23731630.17262632X-RAY DIFFRACTION99.71
2.57-2.710.23351570.1752630X-RAY DIFFRACTION99.96
2.71-2.880.21911450.17192651X-RAY DIFFRACTION100
2.88-3.10.21581500.16862656X-RAY DIFFRACTION99.96
3.1-3.410.1811380.1612697X-RAY DIFFRACTION99.93
3.41-3.90.16071240.14612709X-RAY DIFFRACTION99.93
3.91-4.920.15171590.13032701X-RAY DIFFRACTION99.72
4.92-52.60.18851500.15772866X-RAY DIFFRACTION99.83
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)
11.43773741052-0.907960875704-0.581787516612.53093640353-0.01240426073632.413727772190.129556921630.31446592972-0.0208075949192-0.374267806163-0.1417545526450.116995694115-0.0453388724455-0.1958012249730.02410583561520.1717285811010.0399198527039-0.04106703356250.2026704961970.01270450064380.155109332248-13.747317455214.0974731604-34.4637935254
22.45389147598-1.37750619294-2.108302337323.86061856940.5591606019622.055160071740.104176665462-0.06690993085360.285895471141-0.1408634197280.0712527971883-0.4509010397620.01006800024390.201835808636-0.1212637876910.17323354951-0.03861159634230.003329414202770.1915569970690.02461902695370.1734539896336.9792168304716.6387282219-27.8271477047
31.41119993898-0.492817058626-0.3500431159010.8602903121840.3914092100730.3737280378540.04399781064350.08957897057630.029354908682-0.0963675633186-0.06866986317060.0955465570383-0.0349290600901-0.05683000283520.02768417704180.1389481850890.00946806036673-0.02275283617030.130873642396-0.006020291211430.114400648131-11.09527228728.34377262251-26.1658686262
41.75928762375-0.730498395575-1.080608717470.7687534696470.3845209315841.35513557576-0.0786058726295-0.164355763917-0.1435355734630.07455621849750.0507670032616-0.06078511254160.1207725535050.1808602503250.03521917519150.188595829321-0.00306383376471-0.02069731668540.138671996638-0.002073147624890.1817154203114.21672469402-7.17094150612-18.8013417533
53.02143046167-0.8362112764120.07544610073991.77254705495-0.1838789190950.970067872528-0.012307659304-0.161400118021-0.2882651574910.07023048551930.06283441896080.4076464175510.0540295864324-0.192720579321-0.05605863156380.173362648171-0.04011982264610.0007312916330850.158764063219-0.003989484939150.202321566124-26.077304069-0.807948139798-12.7590295722
65.43540573751-0.336864074518-3.875703006450.416360478517-0.3965640524485.59332585411-0.1373745687450.0370269528975-0.540482955418-0.03266315415930.01459116712760.08412583587620.308477393237-0.1474631001570.2373348169570.209109523883-0.0187887009978-0.03126096466610.0954428579888-0.01077612661040.252810188227-10.6330635767-11.6387731731-20.2297794584
72.46967149306-0.1527415071920.1310700645241.99569025332-0.3354451387071.018309502350.04301914369590.247658037865-0.133880655359-0.118508714184-0.0460963086064-0.1403419919040.03724447807110.0520374898449-0.01544769271460.1716428930570.02290073646180.01214682915940.138479347606-0.03212371686920.14553317909911.5471229976-5.48644765682-34.8354630143
83.20707867096-0.590536305502-0.5802205256229.979157753165.458090927858.12082600505-0.06248558714960.186222791982-0.2846007434380.2339293746880.245809856535-0.6643686508521.008112893490.375498016423-0.1344912024370.3530667228340.0217414562557-0.05680046574070.285346282145-0.001211113617740.26558107902313.08828905391.76634916615-1.11566210985
92.43863656842-0.4438333884890.2347854926213.635067061680.3176878554143.487805730030.0258341581077-0.2939575844670.3143183118580.2940276821270.0723509931145-0.261841853237-0.02544225544740.139701399561-0.1607586783250.130584423007-0.0326828953338-0.02672750580040.167297234438-0.03398269992480.2041553183889.7988544699814.83389885981.92769009004
104.616354434123.733962295530.7104748447464.42309529612-1.158197579883.38668035150.0691814394026-0.4647406742960.1228002608790.0699222592468-0.02316101312610.1436788785180.118068566544-0.326956704032-0.0008808232501430.2255580079140.0203527820249-0.003934823584320.227004394144-0.02000465281820.153052826236-2.3178763416310.96471253740.523924278379
114.373667259240.333574146549-0.225516579383.59748149828-0.1841333864984.24919338787-0.1323071686030.241674918220.6974525152070.03605870226340.102977633690.0709539743997-0.405195547641-0.147930116421-0.003807071940050.1880135093940.0151688852656-0.03447571282250.1100360288970.00182798827740.1777950174925.8523459268320.5827083471-5.34673543375
122.940435152290.63126174126-1.403893516542.897223852880.3537170123233.831614300360.130070072469-0.1114060775920.416262591960.250583711996-0.1251784638740.141866473192-0.273998523521-0.206743206740.01754871711160.1941093171470.0296289441622-0.01788163079430.191841592428-0.0618752906330.1591379632642.6425084721917.3018765154.25133837517
130.0917210642249-0.2518331269540.3204905301162.441459643-2.462664275262.55536760456-0.001592686106280.03030572497550.02028006927-0.1727799450820.01224293288760.06456877071120.09287841175570.09011116402280.01407400743210.231339843638-0.00782252716321-0.01510071214450.184654185063-0.02719216705020.140313395652.5018276870611.6995223027-13.3338974677
143.78623424746-1.24334018119-2.365022970894.838690113693.179231717152.88005037804-0.0902233982994-0.5089187169780.0502216410050.5393292328930.01791055518540.1700976806770.179064529754-0.01741451811480.08103049295760.2470051903920.0134733609034-0.03599226665830.225469453822-0.02022305565160.1438408974322.335244876039.982958080213.9145196694
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 46 )AA2 - 461 - 45
22chain 'A' and (resid 47 through 81 )AA47 - 8146 - 74
33chain 'A' and (resid 82 through 206 )AA82 - 20675 - 199
44chain 'A' and (resid 207 through 281 )AA207 - 281200 - 274
55chain 'A' and (resid 282 through 341 )AA282 - 341275 - 334
66chain 'A' and (resid 342 through 365 )AA342 - 365335 - 358
77chain 'A' and (resid 366 through 441 )AA366 - 441359 - 434
88chain 'D' and (resid -4 through 7 )DE-4 - 71 - 12
99chain 'D' and (resid 8 through 33 )DE8 - 3313 - 38
1010chain 'D' and (resid 34 through 45 )DE34 - 4539 - 50
1111chain 'D' and (resid 46 through 76 )DE46 - 7651 - 81
1212chain 'D' and (resid 77 through 98 )DE77 - 9882 - 103
1313chain 'D' and (resid 99 through 115 )DE99 - 115104 - 120
1414chain 'D' and (resid 116 through 129 )DE116 - 129121 - 134

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