1tzo

Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore

Method: X-RAY DIFFRACTION Dmax: 263.6 Å Quality: GOOD

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

Protective antigen

Bacillus anthracis str.

UniProt P13423

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 203–764 Chain B; UniProt 203–764 Chain C; UniProt 203–764 Chain D; UniProt 203–764 Chain E; UniProt 203–764 Chain F; UniProt 203–764 Chain O; UniProt 203–764 Fragment:63-kDa domain CA CALCIUM ION × 14 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.25;298 K;HEPES, sodium chloride, b-octylglucoside, spermine, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.60 Å R-free 0.317
2 Protein homooligomer Homooligomer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain G; UniProt 203–764 Chain H; UniProt 203–764 Chain I; UniProt 203–764 Chain J; UniProt 203–764 Chain K; UniProt 203–764 Chain L; UniProt 203–764 Chain M; UniProt 203–764 Fragment:63-kDa domain CA CALCIUM ION × 14 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.25;298 K;HEPES, sodium chloride, b-octylglucoside, spermine, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.60 Å R-free 0.317

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.

28 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAG_BACAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–562; UniProt 203–764 Author chain B; PDBConstruct 1–562; UniProt 203–764 Author chain C; PDBConstruct 1–562; UniProt 203–764 Author chain D; PDBConstruct 1–562; UniProt 203–764 Author chain E; PDBConstruct 1–562; UniProt 203–764 Author chain F; PDBConstruct 1–562; UniProt 203–764 Author chain G; PDBConstruct 1–562; UniProt 203–764 Author chain H; PDBConstruct 1–562; UniProt 203–764 Author chain I; PDBConstruct 1–562; UniProt 203–764 Author chain J; PDBConstruct 1–562; UniProt 203–764 Author chain K; PDBConstruct 1–562; UniProt 203–764 Author chain L; PDBConstruct 1–562; UniProt 203–764 Author chain M; PDBConstruct 1–562; UniProt 203–764 Author chain O; PDBConstruct 1–562; UniProt 203–764

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 1tzo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1tzo
Deposition date deposition_date2004-07-10
Structure title titleCrystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore
Keywords keywordsheptamer, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier98.41
Radius of gyration Rg (electron density) rg_electron99.78
Forward intensity I(0) i010564500000.00
Molecular weight molecular_weight867760.0 kDa
Excluded volume excluded_volume1082100 ų
Envelope volume envelope_volume1939700 ų
Hydration-shell volume shell_volume159500 ų
Envelope diameter envelope_diameter330.9
Shell Rg shell_rg97.99
Envelope Rg envelope_rg95.61
Shape Rg shape_rg99.78
Total Rg total_rg99.77
Total atoms total_atoms61138
Residues n_residues7742
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 dmax263.6
Rg (real space) rg_real94.57
Rg uncertainty (real space) rg_real_error1.20
I(0) (real space) i0_real1.0140e+10
I(0) uncertainty (real space) i0_real_error2.0610e+08
Rg (reciprocal space) rg_reciprocal91.88
I(0) (reciprocal space) i0_reciprocal10330000000.0000
Solution quality estimate total_estimate0.8471
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary65.9
Skewness Skewness skewness0.304
Kurtosis Kurtosis kurtosis-1.032
Angular range angular_range— – 0.0800 −1
Current regularization parameter α current_alpha0.9071
Highest regularization parameter α highest_alpha538000000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.758; Stabil: 0.939; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 70 domains

SCOP 2.08 (28 domains)

Domain ID domain_idd1tzoa1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoa2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzob1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzob2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzoc1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoc2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzod1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzod2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzoe1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoe2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzof1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzof2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzog1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzog2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzoh1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoh2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzoi1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoi2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzoj1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoj2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzok1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzok2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzol1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzol2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzom1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzom2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd1tzoo1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.60 — Anthrax protective antigen C-terminal-like
Superfamily Superfamily superfamilyf.60.1 — Anthrax protective antigen C-terminal-like
Family Family familyf.60.1.1 — Anthrax protective antigen C-terminal-like
Domain ID domain_idd1tzoo2
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14

CATH v4.4 (42 domains)

Domain ID domain_id1tzoA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoB04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoC03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoC04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoD03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoD04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoE03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoE04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoF03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoF04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoG03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoG04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoH03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoH04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoI03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoI04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoJ03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoJ04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoK03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoK04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoL03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoL04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoM02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoM03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoM04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id1tzoO02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily240 — Protective antigen, heptamerisation domain
Domain ID domain_id1tzoO03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily110
Domain ID domain_id1tzoO04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810

8. Citations (1)

9. Files and Curves (10)