1xfu

Crystal structure of anthrax edema factor (EF) truncation mutant, EF-delta 64 in complex with calmodulin

Method: X-RAY DIFFRACTION Dmax: 305.4 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 64–800 Mutation:detetion of 33-63 Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 3 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 3.35 Å R-free 0.300
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 64–800 Mutation:detetion of 33-63 Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 3 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 3.35 Å R-free 0.300
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 64–800 Mutation:detetion of 33-63 Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 3 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 3.35 Å R-free 0.300
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 64–800 Mutation:detetion of 33-63 Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 3 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 3.35 Å R-free 0.300
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 64–800 Mutation:detetion of 33-63 Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 3 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 3.35 Å R-free 0.300
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 64–800 Mutation:detetion of 33-63 Calmodulin 2 × 1 (P62158) MG MAGNESIUM ION × 1 CA CALCIUM ION × 3 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 3.35 Å R-free 0.300

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 11–747; UniProt 64–800 Author chain B; PDBConstruct 11–747; UniProt 64–800 Author chain C; PDBConstruct 11–747; UniProt 64–800 Author chain D; PDBConstruct 11–747; UniProt 64–800 Author chain E; PDBConstruct 11–747; UniProt 64–800 Author chain F; PDBConstruct 11–747; UniProt 64–800

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 × 3 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 3.35 Å R-free 0.300
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 × 3 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 3.35 Å R-free 0.300
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 × 3 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 3.35 Å R-free 0.300
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 × 3 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 3.35 Å R-free 0.300
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 × 3 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 3.35 Å R-free 0.300
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 × 3 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 3.35 Å R-free 0.300

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 1xfu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xfu
Deposition date deposition_date2004-09-15
Structure title titleCrystal structure of anthrax edema factor (EF) truncation mutant, EF-delta 64 in complex with calmodulin
Keywords keywordsprotein-protein complex, 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_guinier80.92
Radius of gyration Rg (electron density) rg_electron80.73
Forward intensity I(0) i04978050000.00
Molecular weight molecular_weight607910.0 kDa
Excluded volume excluded_volume764200 ų
Envelope volume envelope_volume1433400 ų
Hydration-shell volume shell_volume150890 ų
Envelope diameter envelope_diameter271.4
Shell Rg shell_rg78.49
Envelope Rg envelope_rg75.68
Shape Rg shape_rg80.73
Total Rg total_rg80.67
Total atoms total_atoms42852
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 dmax305.4
Rg (real space) rg_real84.99
Rg uncertainty (real space) rg_real_error2.43
I(0) (real space) i0_real5.0200e+09
I(0) uncertainty (real space) i0_real_error1.1050e+08
Rg (reciprocal space) rg_reciprocal81.53
I(0) (reciprocal space) i0_reciprocal4986000000.0000
Solution quality estimate total_estimate0.8734
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary96.4
Skewness Skewness skewness0.515
Kurtosis Kurtosis kurtosis0.421
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha0.6784
Highest regularization parameter α highest_alpha204500000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.711; Stabil: 0.888; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.859

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_idd1xfuo1
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_idd1xfup1
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_idd1xfuq1
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_idd1xfur1
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_idd1xfus1
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_idd1xfut1
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_id1xfuA01
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_id1xfuA03
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_id1xfuA04
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_id1xfuB01
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_id1xfuB03
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_id1xfuB04
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_id1xfuC01
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_id1xfuC03
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_id1xfuC04
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_id1xfuD01
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_id1xfuD03
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_id1xfuD04
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_id1xfuE01
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_id1xfuE03
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_id1xfuE04
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_id1xfuF01
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_id1xfuF03
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_id1xfuF04
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_id1xfuO01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuO02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuP01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuP02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuQ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuQ02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuR01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuR02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuS01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuS02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuT01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1xfuT02
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)