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- PDB-1pto: THE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR R... -

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Basic information

Entry
Database: PDB / ID: 1pto
TitleTHE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR RECEPTOR BINDING
Components
  • (PERTUSSIS TOXIN (SUBUNIT ...) x 4
  • (PERTUSSIS TOXIN) x 2
KeywordsTOXIN
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Pentosyltransferases / : / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / 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
: / Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 4 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsStein, P.E. / Read, R.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Structure of a pertussis toxin-sugar complex as a model for receptor binding.
Authors: Stein, P.E. / Boodhoo, A. / Armstrong, G.D. / Heerze, L.D. / Cockle, S.A. / Klein, M.H. / Read, R.J.
#1: Journal: 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
DepositionMar 22, 1994Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700SHEET STRAND 2 MAKES HYDROGEN BONDS WITH STRAND 1 OF SHEET B5 AND ALSO WITH STRAND 2 OF SHEET B7. ...SHEET STRAND 2 MAKES HYDROGEN BONDS WITH STRAND 1 OF SHEET B5 AND ALSO WITH STRAND 2 OF SHEET B7. STRAND 2 MAKES HYDROGEN BONDS WITH STRAND 1 OF SHEET B9 AND ALSO WITH STRAND 2 OF SHEET B11.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERTUSSIS TOXIN (SUBUNIT S1)
B: PERTUSSIS TOXIN
C: PERTUSSIS TOXIN
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
J: PERTUSSIS TOXIN (SUBUNIT S4)
K: PERTUSSIS TOXIN (SUBUNIT S4)
L: PERTUSSIS TOXIN (SUBUNIT S5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,51215
Polymers211,09812
Non-polymers1,4143
Water00
1
A: PERTUSSIS TOXIN (SUBUNIT S1)
B: PERTUSSIS TOXIN
C: PERTUSSIS TOXIN
D: PERTUSSIS TOXIN (SUBUNIT S4)
E: PERTUSSIS TOXIN (SUBUNIT S4)
F: PERTUSSIS TOXIN (SUBUNIT S5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3938
Polymers105,4506
Non-polymers9432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-86 kcal/mol
Surface area35040 Å2
MethodPISA
2
G: PERTUSSIS TOXIN (SUBUNIT S1)
H: PERTUSSIS TOXIN (SUBUNIT S2)
I: PERTUSSIS TOXIN
J: PERTUSSIS TOXIN (SUBUNIT S4)
K: PERTUSSIS TOXIN (SUBUNIT S4)
L: PERTUSSIS TOXIN (SUBUNIT S5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1207
Polymers105,6486
Non-polymers4711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-88 kcal/mol
Surface area34940 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: (-0.9225, 0.3548, -0.1517), (0.36, 0.6499, -0.6694), (-0.1389, -0.6721, -0.7273)
Vector: 18.467, 21.371, 61.775)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 2 .. A 235 G 2 .. G 235 0.916 M1 B 4 .. B 199 H 4 .. H 199 0.659 M1 C 4 .. C 199 I 4 .. I 199 0.916 M1 D 1 .. D 110 J 1 .. J 110 0.554 M1 E 1 .. E 110 K 1 .. K 110 1.009 M1 F 2 .. F 99 L 2 .. L 99 0.955

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Components

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PERTUSSIS TOXIN (SUBUNIT ... , 4 types, 9 molecules AGDEJKFLH

#1: Protein PERTUSSIS TOXIN (SUBUNIT S1)


Mass: 27129.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bordetella pertussis (bacteria) / Cell line: S2 / References: EMBL: X16347, UniProt: P04977*PLUS
#4: Protein
PERTUSSIS TOXIN (SUBUNIT S4)


Mass: 12072.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bordetella pertussis (bacteria) / Cell line: S2 / References: UniProt: P04980, UniProt: P0A3R5*PLUS
#5: Protein PERTUSSIS TOXIN (SUBUNIT S5)


Mass: 10894.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bordetella pertussis (bacteria) / Cell line: S2 / References: UniProt: P04981
#6: Protein PERTUSSIS TOXIN (SUBUNIT S2)


Mass: 21856.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bordetella pertussis (bacteria) / Cell line: S2 / References: UniProt: P04978

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Protein , 2 types, 3 molecules BCI

#2: Protein PERTUSSIS TOXIN


Mass: 21658.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: SACCHARIDE CONTAINS TERMINAL N-ACETYLNEURAMINIC ACID (ALPHA 2,6) GALACTOSE
Source: (natural) Bordetella pertussis (bacteria) / Cell line: S2 / References: UniProt: P04978
#3: Protein PERTUSSIS TOXIN


Mass: 21622.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SACCHARIDE CONTAINS TERMINAL N-ACETYLNEURAMINIC ACID (ALPHA 2,6) GALACTOSE
Source: (natural) Bordetella pertussis (bacteria) / Cell line: S2 / References: UniProt: P04979

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Sugars , 1 types, 3 molecules

#7: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: Stein, P.E., (1994) Structure, 2, 45.
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
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 10 Å / % possible obs: 87 % / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 34503
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14520 0 96 0 14616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.9
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2

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