6ro0

CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT.

Method: X-RAY DIFFRACTION D_max: 156.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pertussis toxin subunit 1

Bordetella pertussis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–269 Chain G； UniProt 1–269	Mutation：R9K, E129G	Islet-activating protein S2 × 2 （A0A0E8DFW5） Islet-activating protein S3 × 2 （Q546I1） Islet-activating protein S4 × 4 （C0MPK8） Pertussis toxin subunit 5 × 2 （C0MPK9） GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6RO0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	T1SR96_BORPT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–269； UniProt 1–269 Author chain G； PDBConstruct 1–269； UniProt 1–269

Islet-activating protein S2

Bordetella pertussis

UniProt A0A0E8DFW5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain B； UniProt 1–226 Chain H； UniProt 1–226	Not recorded	Pertussis toxin subunit 1 × 2 （T1SR96） Islet-activating protein S3 × 2 （Q546I1） Islet-activating protein S4 × 4 （C0MPK8） Pertussis toxin subunit 5 × 2 （C0MPK9） GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6RO0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0E8DFW5_BORPT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–226； UniProt 1–226 Author chain H； PDBConstruct 1–226； UniProt 1–226

Islet-activating protein S3

Bordetella pertussis

UniProt Q546I1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 1–227 Chain I； UniProt 1–227	Not recorded	Pertussis toxin subunit 1 × 2 （T1SR96） Islet-activating protein S2 × 2 （A0A0E8DFW5） Islet-activating protein S4 × 4 （C0MPK8） Pertussis toxin subunit 5 × 2 （C0MPK9） GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q546I1_BORPT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–227； UniProt 1–227 Author chain I； PDBConstruct 1–227； UniProt 1–227

Islet-activating protein S4

Bordetella pertussis

UniProt C0MPK8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain D； UniProt 1–152 Chain E； UniProt 1–152 Chain J； UniProt 1–152 Chain K； UniProt 1–152	Not recorded	Pertussis toxin subunit 1 × 2 （T1SR96） Islet-activating protein S2 × 2 （A0A0E8DFW5） Islet-activating protein S3 × 2 （Q546I1） Pertussis toxin subunit 5 × 2 （C0MPK9） GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	C0MPK8_BORPT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–152； UniProt 1–152 Author chain E； PDBConstruct 1–152； UniProt 1–152 Author chain J； PDBConstruct 1–152； UniProt 1–152 Author chain K； PDBConstruct 1–152； UniProt 1–152

Pertussis toxin subunit 5

Bordetella pertussis

UniProt C0MPK9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain F； UniProt 1–133 Chain L； UniProt 1–133	Not recorded	Pertussis toxin subunit 1 × 2 （T1SR96） Islet-activating protein S2 × 2 （A0A0E8DFW5） Islet-activating protein S3 × 2 （Q546I1） Islet-activating protein S4 × 4 （C0MPK8） GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	C0MPK9_BORPT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–133； UniProt 1–133 Author chain L； PDBConstruct 1–133； UniProt 1–133

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ro0
Deposition date deposition_date	2019-05-10
Structure title title	CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT.
Keywords keywords	TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.07 Å
Radius of gyration Rg (electron density) rg_electron	51.33 Å
Forward intensity I(0) i0	629115000.00
Molecular weight molecular_weight	207500.0 kDa
Excluded volume excluded_volume	259060 Å³
Envelope volume envelope_volume	343530 Å³
Hydration-shell volume shell_volume	57949 Å³
Envelope diameter envelope_diameter	172.2 Å
Shell Rg shell_rg	50.82 Å
Envelope Rg envelope_rg	50.92 Å
Shape Rg shape_rg	51.38 Å
Total Rg total_rg	51.15 Å
Total atoms total_atoms	14632
Residues n_residues	1871
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	156.9 Å
Rg (real space) rg_real	51.41 Å
Rg uncertainty (real space) rg_real_error	1.38 Å
I(0) (real space) i0_real	6.2910e+08
I(0) uncertainty (real space) i0_real_error	1.0940e+07
Rg (reciprocal space) rg_reciprocal	50.77 Å
I(0) (reciprocal space) i0_reciprocal	628600000.0000
Solution quality estimate total_estimate	0.7716
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.5 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.816
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58760000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.749; Smooth: 0.001

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Pertussis toxin subunit 1
Molecular weight formula_weight	29905.1 kDa
Mutation mutation	R9K, E129G
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G
Atom count atom_count	15156

MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYKYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSGYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQAESSEAMAAWSERAGEAMVLVYYESIAYSF

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 2 Entity 2 polymer

Description description	Islet-activating protein S2
Molecular weight formula_weight	24856.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H

MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 3 Entity 3 polymer

Description description	Islet-activating protein S3
Molecular weight formula_weight	25012.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I

MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTVAELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRLLYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 4 Entity 4 polymer

Description description	Islet-activating protein S4
Molecular weight formula_weight	16566.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,J,K

MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAMKPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 5 Entity 5 polymer

Description description	Pertussis toxin subunit 5
Molecular weight formula_weight	14513.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,L

MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEFCLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDLLELQICPLNGYCE

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d6ro0a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d6ro0b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.2 — Aerolysin/Pertussis toxin (APT) domain

Domain ID domain_id	d6ro0b2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d6ro0c2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0d_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0e_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0f_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d6ro0h1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.2 — Aerolysin/Pertussis toxin (APT) domain

Domain ID domain_id	d6ro0h2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0i1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d6ro0i2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0j_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0k_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d6ro0l_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

CATH v4.4 (16 domains)

Domain ID domain_id	6ro0A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	6ro0B01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	6ro0B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0C01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	6ro0C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0E00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0F00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0G00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	6ro0H01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	6ro0H02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0I01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	6ro0I02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0J00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0K00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6ro0L00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

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8. Citations (1)

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Unit-cell length a length_a	94.464 Å
Unit-cell length b length_b	160.798 Å
Unit-cell length c length_c	194.829 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	46.620 Å
R factor r_factor	0.2410
R_work r_work	0.2400
R_free r_free	0.2600

fit	/app/data/saxs_computation/ro/6ro0/6ro0.fit
pddf	/app/data/pr_computation/ro/6ro0/6ro0.pr.out
profile	/app/data/saxs_computation/ro/6ro0/6ro0.dat

CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT.

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pertussis toxin subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Islet-activating protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Islet-activating protein S3

State in the Current Structure

Other States of the Same Protein in the Database

Islet-activating protein S4

State in the Current Structure

Other States of the Same Protein in the Database

Pertussis toxin subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)