1he1

Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac

Method: X-RAY DIFFRACTION Dmax: 99.1 Å Quality: GOOD

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

EXOENZYME S

PSEUDOMONAS AERUGINOSA

UniProt Q51451

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 95–229 Fragment:96-234, GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 × 1 (P15154) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 95–229 Fragment:96-234, GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 × 1 (P15154) 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

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.

4 other PDB entries and 6 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 1–135; UniProt 95–229 Author chain B; PDBConstruct 1–135; UniProt 95–229

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1

HOMO SAPIENS

UniProt P15154

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–176 Fragment:2-184 EXOENZYME S × 1 (Q51451) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–176 Fragment:2-184 EXOENZYME S × 1 (Q51451) 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

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAC1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–176; UniProt 1–176 Author chain D; PDBConstruct 1–176; UniProt 1–176

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

SAXS profile for 1he1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1he1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1he1
Deposition date deposition_date2000-11-18
Structure title titleCrystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac
Keywords keywords;SIGNALING PROTEIN, SIGNALLING COMPLEX, EXOS, RAC, PSEUDOMONAS AERUGINOSA, GAP, TOXIN, VIRULENCE FACTOR, TRANSITION STATE, PROTEIN-PROTEIN COMPLEX, GTPASE, SIGNAL TRANSDUCTION ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.43
Radius of gyration Rg (electron density) rg_electron29.02
Forward intensity I(0) i078430700.00
Molecular weight molecular_weight68839.0 kDa
Excluded volume excluded_volume85914 ų
Envelope volume envelope_volume104830 ų
Hydration-shell volume shell_volume31158 ų
Envelope diameter envelope_diameter103.8
Shell Rg shell_rg34.80
Envelope Rg envelope_rg29.10
Shape Rg shape_rg29.03
Total Rg total_rg29.55
Total atoms total_atoms4812
Residues n_residues622
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax99.1
Rg (real space) rg_real29.55
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real7.8430e+07
I(0) uncertainty (real space) i0_real_error1.2010e+06
Rg (reciprocal space) rg_reciprocal29.50
I(0) (reciprocal space) i0_reciprocal78430000.0000
Solution quality estimate total_estimate0.8019
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5
Skewness Skewness skewness0.444
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37560000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1he1a1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.11 — Bacterial GAP domain
Family Family familya.24.11.1 — Bacterial GAP domain
Domain ID domain_idd1he1a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1he1b1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.11 — Bacterial GAP domain
Family Family familya.24.11.1 — Bacterial GAP domain
Domain ID domain_idd1he1b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1he1c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1he1c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1he1d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1he1d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id1he1A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily260 — Virulence factor YopE uncharacterised domain
Domain ID domain_id1he1B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily260 — Virulence factor YopE uncharacterised domain
Domain ID domain_id1he1C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1he1D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)