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- PDB-1prt: THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN -

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Basic information

Entry
Database: PDB / ID: 1prt
TitleTHE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN
Components
  • PERTUSSIS TOXIN (SUBUNIT S1)
  • PERTUSSIS TOXIN (SUBUNIT S2)
  • PERTUSSIS TOXIN (SUBUNIT S3)
  • PERTUSSIS TOXIN (SUBUNIT S4)
  • PERTUSSIS TOXIN (SUBUNIT S5)
KeywordsTOXIN
Function / homology
Function and homology information


symbiont-mediated activation of host MAPK cascade / symbiont-mediated activation of host G protein-coupled receptor signal transduction / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A ...Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / 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
Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsStein, P.E. / Read, R.J.
CitationJournal: Structure / Year: 1994
Title: The crystal structure of pertussis toxin.
Authors: Stein, P.E. / Boodhoo, A. / Armstrong, G.D. / Cockle, S.A. / Klein, M.H. / Read, R.J.
History
DepositionNov 22, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET STRAND 2 OF SHEET *B1B* ALSO MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3B*. LIKEWISE ...SHEET STRAND 2 OF SHEET *B1B* ALSO MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3B*. LIKEWISE STRAND 2 OF SHEET *B1H* MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3H*. STRAND 2 OF SHEET *B1C* ALSO MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3C*. LIKEWISE STRAND 2 OF SHEET *B1I* MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3I*.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PERTUSSIS TOXIN (SUBUNIT S1)
B: PERTUSSIS TOXIN (SUBUNIT S2)
C: PERTUSSIS TOXIN (SUBUNIT S3)
D: PERTUSSIS TOXIN (SUBUNIT S4)
E: PERTUSSIS TOXIN (SUBUNIT S4)
F: PERTUSSIS TOXIN (SUBUNIT S5)
G: PERTUSSIS TOXIN (SUBUNIT S1)
H: PERTUSSIS TOXIN (SUBUNIT S2)
I: PERTUSSIS TOXIN (SUBUNIT S3)
J: PERTUSSIS TOXIN (SUBUNIT S4)
K: PERTUSSIS TOXIN (SUBUNIT S4)
L: PERTUSSIS TOXIN (SUBUNIT S5)


Theoretical massNumber of molelcules
Total (without water)208,90812
Polymers208,90812
Non-polymers00
Water00
1
A: PERTUSSIS TOXIN (SUBUNIT S1)
B: PERTUSSIS TOXIN (SUBUNIT S2)
C: PERTUSSIS TOXIN (SUBUNIT S3)
D: PERTUSSIS TOXIN (SUBUNIT S4)
E: PERTUSSIS TOXIN (SUBUNIT S4)
F: PERTUSSIS TOXIN (SUBUNIT S5)


Theoretical massNumber of molelcules
Total (without water)104,4546
Polymers104,4546
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-87 kcal/mol
Surface area35050 Å2
MethodPISA
2
G: PERTUSSIS TOXIN (SUBUNIT S1)
H: PERTUSSIS TOXIN (SUBUNIT S2)
I: PERTUSSIS TOXIN (SUBUNIT S3)
J: PERTUSSIS TOXIN (SUBUNIT S4)
K: PERTUSSIS TOXIN (SUBUNIT S4)
L: PERTUSSIS TOXIN (SUBUNIT S5)


Theoretical massNumber of molelcules
Total (without water)104,4546
Polymers104,4546
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15100 Å2
ΔGint-88 kcal/mol
Surface area35110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.800, 98.200, 194.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 196 / 2: CIS PROLINE - PRO D 84 / 3: CIS PROLINE - PRO E 84 / 4: CIS PROLINE - PRO G 196 / 5: CIS PROLINE - PRO J 84 / 6: CIS PROLINE - PRO K 84
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9153, 0.3679, -0.163799), (0.3764, 0.6368, -0.673), (-0.1433, -0.677599, -0.7213)
Vector: 18.363, 21.556, 61.904)
DetailsEACH OF THE TWO HOLOTOXIN MOLECULES IN THE ASYMMETRIC UNIT CONSISTS OF SIX SUBUNITS AND THEY HAVE BEEN ASSIGNED CHAIN INDICATORS A - F AND G - L, RESPECTIVELY. SUBUNIT S1 OF EACH MOLECULE (CHAINS A AND G) FORMS THE ENZYMATIC PART OF THE TOXIN. THE REMAINING FIVE SUBUNITS S2, S3, TWO COPIES OF S4, AND S5 (CHAINS B - F AND H - L) FORM THE CELL-BINDING PART OF THE TOXIN. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A - F WHEN APPLIED TO CHAINS G - L.

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Components

#1: Protein PERTUSSIS TOXIN (SUBUNIT S1)


Mass: 26133.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04977
#2: Protein PERTUSSIS TOXIN (SUBUNIT S2)


Mass: 21658.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04978
#3: Protein PERTUSSIS TOXIN (SUBUNIT S3)


Mass: 21622.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04979
#4: Protein
PERTUSSIS TOXIN (SUBUNIT S4)


Mass: 12072.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P0A3R5
#5: Protein PERTUSSIS TOXIN (SUBUNIT S5)


Mass: 10894.472 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04981
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 mMsodium potassium phosphate1reservoir
20.25 M1reservoirKCl
30.02 %1reservoirNaN3
40.3-0.5 M1reservoirKClprecipitant

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→10 Å / Rfactor Rwork: 0.195 / Rfactor obs: 0.195 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14504 0 0 0 14504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.8

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