3etb

Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4

Method: X-RAY DIFFRACTION Dmax: 175.6 Å Quality: GOOD

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

Anthrax Protective Antigen

Bacillus anthracis

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain J; UniProt 621–764 Fragment:Domain 4 of protective antigen PA-63: UNP residues 621-764 Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.80 Å R-free 0.276
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain K; UniProt 621–764 Fragment:Domain 4 of protective antigen PA-63: UNP residues 621-764 Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.80 Å R-free 0.276
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 621–764 Fragment:Domain 4 of protective antigen PA-63: UNP residues 621-764 Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.80 Å R-free 0.276
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain M; UniProt 621–764 Fragment:Domain 4 of protective antigen PA-63: UNP residues 621-764 Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.80 Å R-free 0.276

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 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAG_BACAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain J; PDBConstruct 1–144; UniProt 621–764 Author chain K; PDBConstruct 1–144; UniProt 621–764 Author chain L; PDBConstruct 1–144; UniProt 621–764 Author chain M; PDBConstruct 1–144; UniProt 621–764

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 3etb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3etb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3etb
Deposition date deposition_date2008-10-07
Structure title titleCrystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4
Keywords keywordssingle-chain FV, monoclonal antibody, immunoglobulin, toxin, antibody-antigen complex, IMMUNE SYSTEM-TOXIN COMPLEX; IMMUNE SYSTEM/TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier49.43
Radius of gyration Rg (electron density) rg_electron50.44
Forward intensity I(0) i0407684000.00
Molecular weight molecular_weight163840.0 kDa
Excluded volume excluded_volume203830 ų
Envelope volume envelope_volume292110 ų
Hydration-shell volume shell_volume52567 ų
Envelope diameter envelope_diameter185.8
Shell Rg shell_rg47.52
Envelope Rg envelope_rg50.09
Shape Rg shape_rg50.44
Total Rg total_rg50.35
Total atoms total_atoms11546
Residues n_residues1465
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 dmax175.6
Rg (real space) rg_real50.26
Rg uncertainty (real space) rg_real_error2.67
I(0) (real space) i0_real4.0770e+08
I(0) uncertainty (real space) i0_real_error8.9920e+06
Rg (reciprocal space) rg_reciprocal49.44
I(0) (reciprocal space) i0_reciprocal407200000.0000
Solution quality estimate total_estimate0.7799
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.4
Skewness Skewness skewness0.566
Kurtosis Kurtosis kurtosis-0.335
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20370000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.652; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.629; Smooth: 0.551

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3etbF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3etbJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id3etbK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id3etbL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810
Domain ID domain_id3etbM00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily810

8. Citations (1)

9. Files and Curves (10)