1s26

Structure of Anthrax Edema Factor-Calmodulin-alpha,beta-methyleneadenosine 5'-triphosphate Complex Reveals an Alternative Mode of ATP Binding to the Catalytic Site

Method: X-RAY DIFFRACTION Dmax: 124.6 Å Quality: GOOD

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

Calmodulin-sensitive adenylate cyclase

Bacillus anthracis

UniProt P40136

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 291–800 Fragment:RESIDUE 291-800, C-TERMINAL EF3 Calmodulin × 1 (P62158) YB YTTERBIUM (III) ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;PEG 8000, Ammonium Sulfate, Glycerol, cacodylate, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP Resolution 3.00 Å R-free 0.304
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 291–800 Fragment:RESIDUE 291-800, C-TERMINAL EF3 Calmodulin × 1 (P62158) YB YTTERBIUM (III) ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;PEG 8000, Ammonium Sulfate, Glycerol, cacodylate, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP Resolution 3.00 Å R-free 0.304
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 291–800 Fragment:RESIDUE 291-800, C-TERMINAL EF3 Calmodulin × 1 (P62158) YB YTTERBIUM (III) ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;PEG 8000, Ammonium Sulfate, Glycerol, cacodylate, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP Resolution 3.00 Å R-free 0.304

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.

17 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYAA_BACAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–510; UniProt 291–800 Author chain B; PDBConstruct 1–510; UniProt 291–800 Author chain C; PDBConstruct 1–510; UniProt 291–800

Calmodulin

Homo sapiens

UniProt P62158

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 D; UniProt 1–148 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) YB YTTERBIUM (III) ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;PEG 8000, Ammonium Sulfate, Glycerol, cacodylate, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP Resolution 3.00 Å R-free 0.304
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–148 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) YB YTTERBIUM (III) ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;PEG 8000, Ammonium Sulfate, Glycerol, cacodylate, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP Resolution 3.00 Å R-free 0.304
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–148 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) YB YTTERBIUM (III) ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;PEG 8000, Ammonium Sulfate, Glycerol, cacodylate, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP Resolution 3.00 Å R-free 0.304

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.

105 other PDB entries and 174 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–148; UniProt 1–148 Author chain E; PDBConstruct 1–148; UniProt 1–148 Author chain F; PDBConstruct 1–148; UniProt 1–148

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 1s26

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1s26
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1s26
Deposition date deposition_date2004-01-08
Structure title titleStructure of Anthrax Edema Factor-Calmodulin-alpha,beta-methyleneadenosine 5'-triphosphate Complex Reveals an Alternative Mode of ATP Binding to the Catalytic Site
Keywords keywordsAMPCPP, EDEMA FACTOR, CALMODULIN, TOXIN, LYASE-METAL BINDING PROTEIN COMPLEX; TOXIN,LYASE/METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.22
Radius of gyration Rg (electron density) rg_electron40.74
Forward intensity I(0) i0707547000.00
Molecular weight molecular_weight217980.0 kDa
Excluded volume excluded_volume272600 ų
Envelope volume envelope_volume387210 ų
Hydration-shell volume shell_volume76366 ų
Envelope diameter envelope_diameter129.8
Shell Rg shell_rg49.10
Envelope Rg envelope_rg39.42
Shape Rg shape_rg40.74
Total Rg total_rg41.16
Total atoms total_atoms15317
Residues n_residues1882
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 dmax124.6
Rg (real space) rg_real40.97
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real7.0750e+08
I(0) uncertainty (real space) i0_real_error1.2930e+07
Rg (reciprocal space) rg_reciprocal41.22
I(0) (reciprocal space) i0_reciprocal707700000.0000
Solution quality estimate total_estimate0.8298
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.8
Skewness Skewness skewness0.028
Kurtosis Kurtosis kurtosis-0.551
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha65650000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1s26a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.41 — Adenylylcyclase toxin (the edema factor)
Superfamily Superfamily superfamilye.41.1 — Adenylylcyclase toxin (the edema factor)
Family Family familye.41.1.1 — Adenylylcyclase toxin (the edema factor)
Domain ID domain_idd1s26b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.41 — Adenylylcyclase toxin (the edema factor)
Superfamily Superfamily superfamilye.41.1 — Adenylylcyclase toxin (the edema factor)
Family Family familye.41.1.1 — Adenylylcyclase toxin (the edema factor)
Domain ID domain_idd1s26c_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.41 — Adenylylcyclase toxin (the edema factor)
Superfamily Superfamily superfamilye.41.1 — Adenylylcyclase toxin (the edema factor)
Family Family familye.41.1.1 — Adenylylcyclase toxin (the edema factor)
Domain ID domain_idd1s26d_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like
Domain ID domain_idd1s26e_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like
Domain ID domain_idd1s26f_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like

CATH v4.4 (12 domains)

Domain ID domain_id1s26A02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1760 — Adenylylcyclase toxin fold
Homologous superfamily homologous superfamily10 — Anthrax toxin, edema factor, central domain
Domain ID domain_id1s26A03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily60
Domain ID domain_id1s26B02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1760 — Adenylylcyclase toxin fold
Homologous superfamily homologous superfamily10 — Anthrax toxin, edema factor, central domain
Domain ID domain_id1s26B03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily60
Domain ID domain_id1s26C02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1760 — Adenylylcyclase toxin fold
Homologous superfamily homologous superfamily10 — Anthrax toxin, edema factor, central domain
Domain ID domain_id1s26C03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily60
Domain ID domain_id1s26D01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1s26D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1s26E01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1s26E02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1s26F01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1s26F02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (2)

9. Files and Curves (10)