SAXSdb — 1ikp

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

EXOTOXIN A

Pseudomonas aeruginosa

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 26–638	Mutation：W281A, P201Q	CL CHLORIDE ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；281 K；PEG 8000, sodium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281.0K	Resolution 1.45 Å R-free 0.228

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 1IKP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AER DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH BETA-TAD Deposited 1995-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 425–634（210 aa） Fragment：DOMAIN III OF PSEUDOMONAS TOXIN Chain B 425–634（210 aa） Fragment：DOMAIN III OF PSEUDOMONAS TOXIN	Not recorded	TAD BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE × 2 TIA 2-(1,5-DIDEOXYRIBOSE)-4-AMIDO-THIAZOLE × 2 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.285
1DMA DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH NICOTINAMIDE AND AMP Deposited 1995-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 425–638（214 aa） Chain B 425–638（214 aa）	Not recorded	NCA NICOTINAMIDE × 4 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.265
1IKQ Pseudomonas Aeruginosa Exotoxin A, wild type Deposited 2001-05-04	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–638（613 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；281 K；PEG 8000, sodium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 1.62 Å R-free 0.235
1XK9 Pseudomanas exotoxin A in complex with the PJ34 inhibitor Deposited 2004-09-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 424–638（215 aa） Fragment：catalytic fragment, PE24H	Not recorded	P34 N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；sodium citrate, DTT, NaAzid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.235
1XK9 Pseudomanas exotoxin A in complex with the PJ34 inhibitor Deposited 2004-09-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 424–638（215 aa） Fragment：catalytic fragment, PE24H	Not recorded	P34 N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；sodium citrate, DTT, NaAzid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.235
2ZIT Structure of the eEF2-ExoA-NAD+ complex Deposited 2008-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 425–630（206 aa） Fragment：catalytic domain	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.266
2ZIT Structure of the eEF2-ExoA-NAD+ complex Deposited 2008-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 425–630（206 aa） Fragment：catalytic domain	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.266
2ZIT Structure of the eEF2-ExoA-NAD+ complex Deposited 2008-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 425–630（206 aa） Fragment：catalytic domain	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.266
3B78 Structure of the eEF2-ExoA(R551H)-NAD+ complex Deposited 2007-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 425–630（206 aa） Fragment：catalytic domain	Mutation：R551H	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.242
3B78 Structure of the eEF2-ExoA(R551H)-NAD+ complex Deposited 2007-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 425–630（206 aa） Fragment：catalytic domain	Mutation：R551H	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.242
3B78 Structure of the eEF2-ExoA(R551H)-NAD+ complex Deposited 2007-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 425–630（206 aa） Fragment：catalytic domain	Mutation：R551H	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.242
3B82 Structure of the eEF2-ExoA(E546H)-NAD+ complex Deposited 2007-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 425–630（206 aa） Fragment：catalytic domain	Mutation：E546H	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.35 Å R-free 0.257
3B82 Structure of the eEF2-ExoA(E546H)-NAD+ complex Deposited 2007-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 425–630（206 aa） Fragment：catalytic domain	Mutation：E546H	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.35 Å R-free 0.257
3B82 Structure of the eEF2-ExoA(E546H)-NAD+ complex Deposited 2007-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 425–630（206 aa） Fragment：catalytic domain	Mutation：E546H	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.35 Å R-free 0.257
3B8H Structure of the eEF2-ExoA(E546A)-NAD+ complex Deposited 2007-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 425–630（206 aa） Fragment：catalytic domain	Mutation：E546A	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.256
3B8H Structure of the eEF2-ExoA(E546A)-NAD+ complex Deposited 2007-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 425–630（206 aa） Fragment：catalytic domain	Mutation：E546A	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.256
3B8H Structure of the eEF2-ExoA(E546A)-NAD+ complex Deposited 2007-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 425–630（206 aa） Fragment：catalytic domain	Mutation：E546A	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.256

8 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOXA_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–613； UniProt 26–638

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ikp
Deposition date deposition_date	2001-05-04
Structure title title	Pseudomonas Aeruginosa Exotoxin A, P201Q, W281A mutant
Keywords keywords	all 3 EXOTOXIN A domains, TRANSFERASE; TRANSFERASE
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	27.02 Å
Radius of gyration Rg (electron density) rg_electron	26.00 Å
Forward intensity I(0) i0	73343800.00
Molecular weight molecular_weight	65089.0 kDa
Excluded volume excluded_volume	80689 Å³
Envelope volume envelope_volume	99135 Å³
Hydration-shell volume shell_volume	31877 Å³
Envelope diameter envelope_diameter	92.5 Å
Shell Rg shell_rg	33.33 Å
Envelope Rg envelope_rg	26.13 Å
Shape Rg shape_rg	25.97 Å
Total Rg total_rg	26.84 Å
Total atoms total_atoms	4586
Residues n_residues	599
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	91.6 Å
Rg (real space) rg_real	27.02 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	7.3340e+07
I(0) uncertainty (real space) i0_real_error	1.0680e+06
Rg (reciprocal space) rg_reciprocal	27.02 Å
I(0) (reciprocal space) i0_reciprocal	73340000.0000
Solution quality estimate total_estimate	0.8702
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.251
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19320000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	EXOTOXIN A
Molecular weight formula_weight	66787.8 kDa
EC 编号 ec_number	2.4.2.-
Mutation mutation	W281A, P201Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5185

AEEAFDLWNECAKACVLDLKDGVRSSRMSVDPAIADTNGQGVLHYSMVLEGGNDALKLAIDNALSITSDGLTIRLEGGVEPNKPVRYSYTRQARGSWSLNWLVPIGHEKPSNIKVFIHELNAGNQLSHMSPIYTIEMGDELLAKLARDATFFVRAHESNEMQPTLAISHAGVSVVMAQAQPRREKRWSEWASGKVLCLLDQLDGVYNYLAQQRCNLDDTWEGKIYRVLAGNPAKHDLDIKPTVISHRLHFPEGGSLAALTAHQACHLPLETFTRHRQPRGAEQLEQCGYPVQRLVALYLAARLSWNQVDQVIRNALASPGSGGDLGEAIREQPEQARLALTLAAAESERFVRQGTGNDEAGAANADVVSLTCPVAAGECAGPADSGDALLERNYPTGAEFLGDGGDVSFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRARSQDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTSLTLAAPEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVGGDLDPSSIPDKEQAISALPDYASQPGKPPREDLK

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI Class编号 ncbi_taxonomy_id	287
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	540

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ikpa1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.7 — Exotoxin A, N-terminal domain

Domain ID domain_id	d1ikpa2
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	d1ikpa3
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.5 — Exotoxin A, middle domain
Family Family family	f.1.5.1 — Exotoxin A, middle domain

CATH v4.4 (3 domains)

Domain ID domain_id	1ikpA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1ikpA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1350 — Exotoxin A, middle domain
Homologous superfamily homologous superfamily	10 — Exotoxin A, middle domain

Domain ID domain_id	1ikpA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	175 — Diphtheria Toxin; domain 1
Homologous superfamily homologous superfamily	10 — Diphtheria Toxin, domain 1

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8. Citations (5)

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Unit-cell length a length_a	59.910 Å
Unit-cell length b length_b	99.070 Å
Unit-cell length c length_c	58.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	21.820 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2280

fit	/app/data/saxs_computation/ik/1ikp/1ikp.fit
pddf	/app/data/pr_computation/ik/1ikp/1ikp.pr.out
profile	/app/data/saxs_computation/ik/1ikp/1ikp.dat

Pseudomonas Aeruginosa Exotoxin A, P201Q, W281A mutant

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

EXOTOXIN A

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