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- PDB-6ro0: CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT. -

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Basic information

Entry
Database: PDB / ID: 6ro0
TitleCRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT.
Components
  • (Islet-activating protein ...) x 3
  • (Pertussis toxin subunit ...) x 2
KeywordsTOXIN
Function / homology
Function and homology information


NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / : / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain ...Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / C-type lectin fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Islet-activating protein S2 / Islet-activating protein S4 / Pertussis toxin subunit 5 / Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4 / Islet-activating protein S3 / Pertussis toxin subunit 1
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsBertrand, T.
CitationJournal: Commun Biol / Year: 2020
Title: Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity.
Authors: Ausar, S.F. / Zhu, S. / Duprez, J. / Cohen, M. / Bertrand, T. / Steier, V. / Wilson, D.J. / Li, S. / Sheung, A. / Brookes, R.H. / Pedyczak, A. / Rak, A. / Andrew James, D.
History
DepositionMay 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
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 / _software.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pertussis toxin subunit 1
B: Islet-activating protein S2
C: Islet-activating protein S3
D: Islet-activating protein S4
E: Islet-activating protein S4
F: Pertussis toxin subunit 5
G: Pertussis toxin subunit 1
H: Islet-activating protein S2
I: Islet-activating protein S3
J: Islet-activating protein S4
K: Islet-activating protein S4
L: Pertussis toxin subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,67221
Polymers254,84312
Non-polymers8299
Water9,440524
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34200 Å2
ΔGint-197 kcal/mol
Surface area70210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.464, 160.798, 194.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Pertussis toxin subunit ... , 2 types, 4 molecules AGFL

#1: Protein Pertussis toxin subunit 1 /


Mass: 29905.109 Da / Num. of mol.: 2 / Mutation: R9K, E129G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxA / Production host: Bordetella pertussis (bacteria) / References: UniProt: T1SR96, UniProt: P04977*PLUS
#5: Protein Pertussis toxin subunit 5 / / Pertussis toxin subunit PtxE


Mass: 14513.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria)
Gene: ptxE, ERS004697_00105, ERS004704_00093, ERS004709_00175, ERS005128_00197, ERS005179_00180, ERS014547_00748, ERS014550_01624, ERS018341_00090
Production host: Bordetella pertussis (bacteria) / References: UniProt: C0MPK9, UniProt: P04981*PLUS

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Islet-activating protein ... , 3 types, 8 molecules BHCIDEJK

#2: Protein Islet-activating protein S2 / Pertussis toxin subunit 2


Mass: 24856.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria)
Gene: ptxB, CYO81_20230, ERS004697_00332, ERS004704_00067, ERS004709_00223, ERS005128_00199, ERS005179_00182, ERS014547_00750, NCTC10911_00247
Production host: Bordetella pertussis (bacteria) / References: UniProt: A0A0E8DFW5, UniProt: P04978*PLUS
#3: Protein Islet-activating protein S3 / Pertussis toxin subunit / Pertussis toxin subunit 3 / Pertussis toxin subunit PtxC / Toxin subunit 3


Mass: 25012.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria)
Gene: ptxS3, ptxC, ptxC_1, ptxC_2, CYO81_20245, ERS004697_00106, ERS004704_00094, ERS004709_00174, ERS005128_00196, ERS005179_00179, ERS014547_00747, ERS014550_01623, NCTC10911_00250
Production host: Bordetella pertussis (bacteria) / References: UniProt: Q546I1, UniProt: P04979*PLUS
#4: Protein
Islet-activating protein S4 / Pertussis toxin subunit 4 / Pertussis toxin subunit PtxD


Mass: 16566.744 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria)
Gene: ptxD, CYO81_20235, ERS005128_00198, ERS005179_00181, ERS014547_00749, NCTC10911_00248
Production host: Bordetella pertussis (bacteria) / References: UniProt: C0MPK8, UniProt: P0A3R5*PLUS

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Non-polymers , 2 types, 533 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 278 K / Method: evaporation / pH: 7 / Details: Spontaneous crystallization in plastic bottles / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.13→46.96 Å / Num. obs: 165565 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 50.68 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.5
Reflection shellResolution: 2.13→2.2 Å / Rmerge(I) obs: 1.95 / Num. unique obs: 16119

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Processing

Software
NameVersionClassification
autoBUSTER2.11.7refinement
XDS20171111data reduction
autoPROC1.1.7data scaling
MOLREP11.6.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRT

1prt


Resolution: 2.13→46.62 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.192 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.167
RfactorNum. reflection% reflectionSelection details
Rfree0.26 8309 5.03 %RANDOM
Rwork0.24 ---
obs0.241 165138 99.5 %-
Displacement parametersBiso mean: 64.94 Å2
Baniso -1Baniso -2Baniso -3
1--20.4126 Å20 Å20 Å2
2---1.8244 Å20 Å2
3---22.2369 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.13→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14506 0 54 524 15084
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00714984HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9320385HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5034SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2505HARMONIC5
X-RAY DIFFRACTIONt_it14984HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion18.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1929SEMIHARMONIC5
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_contact16812SEMIHARMONIC4
LS refinement shellResolution: 2.13→2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3219 591 5 %
Rwork0.3207 11225 -
all0.3208 11816 -
obs--97.11 %

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