1xfy

Crystal structure of anthrax edema factor (EF) in complex with calmodulin

Method: X-RAY DIFFRACTION Dmax: 304.3 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 33–800 Not recorded Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 33–800 Not recorded Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 33–800 Not recorded Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 33–800 Not recorded Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 33–800 Not recorded Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 33–800 Not recorded Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289

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 65 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 10–777; UniProt 33–800 Author chain B; PDBConstruct 10–777; UniProt 33–800 Author chain C; PDBConstruct 10–777; UniProt 33–800 Author chain D; PDBConstruct 10–777; UniProt 33–800 Author chain E; PDBConstruct 10–777; UniProt 33–800 Author chain F; PDBConstruct 10–777; UniProt 33–800

Calmodulin 2

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 O; UniProt 1–149 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 1–149 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain Q; UniProt 1–149 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain R; UniProt 1–149 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain S; UniProt 1–149 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain T; UniProt 1–149 Not recorded Calmodulin-sensitive adenylate cyclase × 1 (P40136) MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;278 K;PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 3.30 Å R-free 0.289

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 171 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 O; PDBConstruct 1–149; UniProt 1–149 Author chain P; PDBConstruct 1–149; UniProt 1–149 Author chain Q; PDBConstruct 1–149; UniProt 1–149 Author chain R; PDBConstruct 1–149; UniProt 1–149 Author chain S; PDBConstruct 1–149; UniProt 1–149 Author chain T; PDBConstruct 1–149; UniProt 1–149

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 1xfy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xfy
Deposition date deposition_date2004-09-15
Structure title titleCrystal structure of anthrax edema factor (EF) in complex with calmodulin
Keywords keywordsprotein-protein interaction, LYASE-METAL BINDING PROTEIN COMPLEX; 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_guinier80.63
Radius of gyration Rg (electron density) rg_electron80.43
Forward intensity I(0) i04975160000.00
Molecular weight molecular_weight607670.0 kDa
Excluded volume excluded_volume763890 ų
Envelope volume envelope_volume1421800 ų
Hydration-shell volume shell_volume149980 ų
Envelope diameter envelope_diameter271.4
Shell Rg shell_rg78.41
Envelope Rg envelope_rg75.52
Shape Rg shape_rg80.44
Total Rg total_rg80.37
Total atoms total_atoms42846
Residues n_residues5286
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 dmax304.3
Rg (real space) rg_real84.34
Rg uncertainty (real space) rg_real_error2.30
I(0) (real space) i0_real5.0140e+09
I(0) uncertainty (real space) i0_real_error1.1390e+08
Rg (reciprocal space) rg_reciprocal81.22
I(0) (reciprocal space) i0_reciprocal4983000000.0000
Solution quality estimate total_estimate0.8664
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary96.1
Skewness Skewness skewness0.500
Kurtosis Kurtosis kurtosis0.402
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha0.6095
Highest regularization parameter α highest_alpha202400000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 0.905; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.868

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1xfyo1
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_idd1xfyp1
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_idd1xfyq1
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_idd1xfyr1
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_idd1xfys1
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_idd1xfyt1
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 (30 domains)

Domain ID domain_id1xfyA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1xfyA03
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_id1xfyA04
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_id1xfyB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1xfyB03
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_id1xfyB04
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_id1xfyC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1xfyC03
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_id1xfyC04
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_id1xfyD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1xfyD03
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_id1xfyD04
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_id1xfyE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1xfyE03
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_id1xfyE04
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_id1xfyF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1xfyF03
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_id1xfyF04
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_id1xfyO01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyO02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyP01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyP02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyQ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyQ02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyR01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyR02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyS01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyS02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyT01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfyT02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (1)

9. Files and Curves (10)