1k90

Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP

Method: X-RAY DIFFRACTION

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

CALMODULIN-SENSITIVE ADENYLATE CYCLASE

Bacillus anthracis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CALMODULIN × 3 （P02593） YTTERBIUM (III) ION × 3 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 3 CALCIUM ION × 6 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CALMODULIN × 1 （P02593） YTTERBIUM (III) ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CALMODULIN × 1 （P02593） YTTERBIUM (III) ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	CALMODULIN × 1 （P02593） YTTERBIUM (III) ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

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 P02593

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CALMODULIN-SENSITIVE ADENYLATE CYCLASE × 3 （P40136） YTTERBIUM (III) ION × 3 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 3 CALCIUM ION × 6 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CALMODULIN-SENSITIVE ADENYLATE CYCLASE × 1 （P40136） YTTERBIUM (III) ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CALMODULIN-SENSITIVE ADENYLATE CYCLASE × 1 （P40136） YTTERBIUM (III) ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	CALMODULIN-SENSITIVE ADENYLATE CYCLASE × 1 （P40136） YTTERBIUM (III) ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALM_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 5–148； UniProt 5–148 Author chain E； PDBConstruct 5–148； UniProt 5–148 Author chain F； PDBConstruct 5–148； UniProt 5–148

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1k90
Deposition date deposition_date	2001-10-26
Structure title title	Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP
Keywords keywords	oedema factor adenylyl cyclase anthrax calmodulin, TOXIN, LYASE-METAL BINDING PROTEIN COMPLEX; TOXIN,LYASE/METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1k90__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1k90__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k90__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.91 Å
Rg (electron density)	40.42 Å
Total Rg	40.84 Å
Atom count	15314
Residues	1882
Excluded volume	272520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k90__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k90__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1k90__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1k90__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	CALMODULIN-SENSITIVE ADENYLATE CYCLASE
Molecular weight formula_weight	58810.6 kDa
EC 编号 ec_number	4.6.1.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	15357

DRIDVLKGEKALKASGLVPEHADAFKKIARELNTYILFRPVNKLATNLIKSGVATKGLNVHGKSSDWGPVAGYIPFDQDLSKKHGQQLAVEKGNLENKKSITEHEGEIGKIPLKLDHLRIEELKENGIILKGKKEIDNGKKYYLLESNNQVYEFRISDENNEVQYKTKEGKITVLGEKFNWRNIEVMAKNVEGVLKPLTADYDLFALAPSLTEIKKQIPQKEWDKVVNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEAVKYTGYTGGDVVNHGTEQDNEEFPEKDNEIFIINPEGEFILTKNWEMTGRFIEKNITGKDYLYYFNRSYNKIAPGNKAYIEWTDPITKAKINTIPTSAEFIKNLSSIRRSSNVGVYKDSGDKDEFAKKESVKKIAGYLSDYYNSANHIFSQEKKRKISIFRGIQAYNEIENVLKSKQIAPEYKNYFQYLKERITNQVQLLLTHQKSNIEFKLLYKQLNFTENETDNFEVFQKIIDEK

Source Source

Source organism organism	Bacillus anthracis
NCBI taxonomy ID ncbi_taxonomy_id	1392
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	CALMODULIN
Molecular weight formula_weight	16721.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	YTTERBIUM (III) ION
Molecular weight formula_weight	173.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1k90a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.41 — Adenylylcyclase toxin (the edema factor)
Superfamily Superfamily superfamily	e.41.1 — Adenylylcyclase toxin (the edema factor)
Family Family family	e.41.1.1 — Adenylylcyclase toxin (the edema factor)

Domain ID domain_id	d1k90b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.41 — Adenylylcyclase toxin (the edema factor)
Superfamily Superfamily superfamily	e.41.1 — Adenylylcyclase toxin (the edema factor)
Family Family family	e.41.1.1 — Adenylylcyclase toxin (the edema factor)

Domain ID domain_id	d1k90c_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.41 — Adenylylcyclase toxin (the edema factor)
Superfamily Superfamily superfamily	e.41.1 — Adenylylcyclase toxin (the edema factor)
Family Family family	e.41.1.1 — Adenylylcyclase toxin (the edema factor)

Domain ID domain_id	d1k90d_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

Domain ID domain_id	d1k90e_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

Domain ID domain_id	d1k90f_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

CATH v4.4 (12 domains)

Domain ID domain_id	1k90A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1760 — Adenylylcyclase toxin fold
Homologous superfamily homologous superfamily	10 — Anthrax toxin, edema factor, central domain

Domain ID domain_id	1k90A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1k90B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1760 — Adenylylcyclase toxin fold
Homologous superfamily homologous superfamily	10 — Anthrax toxin, edema factor, central domain

Domain ID domain_id	1k90B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1k90C02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1760 — Adenylylcyclase toxin fold
Homologous superfamily homologous superfamily	10 — Anthrax toxin, edema factor, central domain

Domain ID domain_id	1k90C03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1k90D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1k90D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1k90E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1k90E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1k90F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1k90F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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Unit-cell length a length_a	116.099 Å
Unit-cell length b length_b	166.100 Å
Unit-cell length c length_c	343.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2860

Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP

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

CALMODULIN-SENSITIVE ADENYLATE CYCLASE

State in the Current Structure

Other States of the Same Protein in the Database

CALMODULIN

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1k90__assembly_1__model_1

1k90__assembly_1__model_1 | I(q)

1k90__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP

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

CALMODULIN-SENSITIVE ADENYLATE CYCLASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CALMODULIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1k90__assembly_1__model_1

1k90__assembly_1__model_1 | I(q)

1k90__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)