1k8t

Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF)

Method: X-RAY DIFFRACTION Dmax: 107.0 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 291–800 Not recorded SO4 SULFATE ION × 4 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;277 K;PEG550,Nickle chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.60 Å R-free 0.276
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 291–800 Not recorded SO4 SULFATE ION × 8 NI NICKEL (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;277 K;PEG550,Nickle chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.60 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.

17 other PDB entries and 69 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

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 1k8t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k8t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k8t
Deposition date deposition_date2001-10-25
Structure title titleCrystal structure of the adenylyl cyclase domain of anthrax edema factor (EF)
Keywords keywordsedema factor, adenylyl cyclase, anthrax, calmodulin, TOXIN, LYASE; TOXIN,LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.09
Radius of gyration Rg (electron density) rg_electron28.57
Forward intensity I(0) i052014300.00
Molecular weight molecular_weight57363.0 kDa
Excluded volume excluded_volume72312 ų
Envelope volume envelope_volume95877 ų
Hydration-shell volume shell_volume29251 ų
Envelope diameter envelope_diameter111.8
Shell Rg shell_rg34.24
Envelope Rg envelope_rg28.75
Shape Rg shape_rg28.58
Total Rg total_rg29.13
Total atoms total_atoms4046
Residues n_residues498
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 dmax107.0
Rg (real space) rg_real29.22
Rg uncertainty (real space) rg_real_error1.04
I(0) (real space) i0_real5.2010e+07
I(0) uncertainty (real space) i0_real_error7.9670e+05
Rg (reciprocal space) rg_reciprocal29.17
I(0) (reciprocal space) i0_reciprocal52010000.0000
Solution quality estimate total_estimate0.8307
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.513
Kurtosis Kurtosis kurtosis0.027
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10360000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.695; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.733; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1k8ta_
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)

CATH v4.4 (2 domains)

Domain ID domain_id1k8tA02
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_id1k8tA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily60

8. Citations (1)

9. Files and Curves (10)