SAXSdb — 1he9

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

EXOENZYME S

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 102–235	Fragment：96-234 GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN) Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；MGCL2, (NH4)2SO4, PEG 6000, NA-CACODYLATE PH5.5, pH 5.50	Resolution 2.40 Å R-free 0.265

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 1HE9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HE1 Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac Deposited 2000-11-18	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 A 95–229（135 aa） Fragment：96-234, GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN)	Not recorded	NI NICKEL (II) ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；8% PEG 6000, 3MM NICL2, 100 MM TRIS/HCL PH8.5, pH 8.50	Resolution 2.00 Å R-free 0.224
1HE1 Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac Deposited 2000-11-18	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 B 95–229（135 aa） Fragment：96-234, GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN)	Not recorded	NI NICKEL (II) ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；8% PEG 6000, 3MM NICL2, 100 MM TRIS/HCL PH8.5, pH 8.50	Resolution 2.00 Å R-free 0.224
2C23 14-3-3 Protein Beta (Human) in complex with exoenzyme S peptide Deposited 2005-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 421–431（11 aa） Fragment：14-3-3 BINDING REGION, RESIDUES 421-431	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.05M MGCL2,0.1M HEPES PH7.5, 30% PEG MME 550, pH 8.00	Resolution 2.65 Å R-free 0.286
6GN0 Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, tetrameric crystal form Deposited 2018-05-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 234–453（220 aa） Chain G 234–453（220 aa）	Mutation：E379A, E381A Mutation：E379A, E381A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；12% PEG 3350, 4% Tacsimate	Resolution 3.24 Å R-free 0.294
6GN0 Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, tetrameric crystal form Deposited 2018-05-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 234–453（220 aa） Chain H 234–453（220 aa）	Mutation：E379A, E381A Mutation：E379A, E381A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；12% PEG 3350, 4% Tacsimate	Resolution 3.24 Å R-free 0.294
6Y7T Engineered conjugation of lysine-specific molecular tweezers with ExoS derived peptidic inhibitor enhance affinity towards target protein 14-3-3 through ditopic binding Deposited 2020-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC	Chain D 420–430（11 aa）	Not recorded	NA SODIUM ION × 3 GOL GLYCEROL × 1 TWZ 2-[4-[2-[hydroxy-[[(1R,5S,9S,16R,20R,24S,28S,35R)-22-phosphonooxy-3-tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2,4(21),6(19),7,10,12,14,17,22,25(38),26,29,31,33,36-pentadecaenyl]oxy]phosphoryl]oxyethyl]triazol-1-yl]acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Bis-Tris Propane 0.2M sodium acetate trihydrate 20% PEG1000 10% Glycerol pH 7 Grew at 4 degree Celsius after a few days	Resolution 2.50 Å R-free 0.268
6Y7T Engineered conjugation of lysine-specific molecular tweezers with ExoS derived peptidic inhibitor enhance affinity towards target protein 14-3-3 through ditopic binding Deposited 2020-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC	Chain E 420–430（11 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 1 TWZ 2-[4-[2-[hydroxy-[[(1R,5S,9S,16R,20R,24S,28S,35R)-22-phosphonooxy-3-tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2,4(21),6(19),7,10,12,14,17,22,25(38),26,29,31,33,36-pentadecaenyl]oxy]phosphoryl]oxyethyl]triazol-1-yl]acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Bis-Tris Propane 0.2M sodium acetate trihydrate 20% PEG1000 10% Glycerol pH 7 Grew at 4 degree Celsius after a few days	Resolution 2.50 Å R-free 0.268

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q51451
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 102–235

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	1he9
Deposition date deposition_date	2000-11-21
Structure title title	Crystal structure of the GAP domain of the Pseudomonas aeruginosa ExoS toxin
Keywords keywords	TOXIN (EXOENZYME S), EXOS, PSEUDOMONAS AERUGINOSA, GAP, TOXIN, VIRULENCE FACTOR, SIGNAL TRANSDUCTION; TOXIN (EXOENZYME S)
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	16.49 Å
Radius of gyration Rg (electron density) rg_electron	15.54 Å
Forward intensity I(0) i0	4481820.00
Molecular weight molecular_weight	14418.0 kDa
Excluded volume excluded_volume	17732 Å³
Envelope volume envelope_volume	20531 Å³
Hydration-shell volume shell_volume	11874 Å³
Envelope diameter envelope_diameter	57.9 Å
Shell Rg shell_rg	20.40 Å
Envelope Rg envelope_rg	15.95 Å
Shape Rg shape_rg	15.53 Å
Total Rg total_rg	16.47 Å
Total atoms total_atoms	1000
Residues n_residues	131
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	59.5 Å
Rg (real space) rg_real	16.55 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	4.4820e+06
I(0) uncertainty (real space) i0_real_error	5.3540e+04
Rg (reciprocal space) rg_reciprocal	16.55 Å
I(0) (reciprocal space) i0_reciprocal	4482000.0000
Solution quality estimate total_estimate	0.7434
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.3 Å
Skewness Skewness skewness	0.499
Kurtosis Kurtosis kurtosis	-0.009
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1031000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1he9a1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.11 — Bacterial GAP domain
Family Family family	a.24.11.1 — Bacterial GAP domain

Domain ID domain_id	d1he9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1he9A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	260 — Virulence factor YopE uncharacterised domain

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8. Citations (1)

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Unit-cell length a length_a	42.897 Å
Unit-cell length b length_b	55.646 Å
Unit-cell length c length_c	107.472 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2570
R_work r_work	0.2570
R_free r_free	0.2650

Description description	EXOENZYME S
Molecular weight formula_weight	14432.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1065

Crystal structure of the GAP domain of the Pseudomonas aeruginosa ExoS toxin

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

EXOENZYME S

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	PSEUDOMONAS AERUGINOSA
NCBI Class编号 ncbi_taxonomy_id	287
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

fit	/app/data/saxs_computation/he/1he9/1he9.fit
pddf	/app/data/pr_computation/he/1he9/1he9.pr.out
profile	/app/data/saxs_computation/he/1he9/1he9.dat