SAXSdb — 8k9z

▼

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

RDTND-RID CBD

Vibrio vulnificus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Calmodulin-2 × 1 （P0DP24） CALCIUM ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Calmodulin-2 × 1 （P0DP24） CALCIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MARTX_VIBVL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–405； UniProt 1967–2371 Author chain C； PDBConstruct 1–405； UniProt 1967–2371

Calmodulin-2

Homo sapiens

UniProt P0DP24

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	RDTND-RID CBD × 1 （A0A2S3R7M0） CALCIUM ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RDTND-RID CBD × 1 （A0A2S3R7M0） CALCIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–151； UniProt 1–149 Author chain D； PDBConstruct 3–151； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8k9z
Deposition date deposition_date	2023-08-02
Structure title title	Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin
Keywords keywords	MARTX toxin, RDTND-RID, NADase, CaM, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8k9z__assembly_1__model_1

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

Download this curve (.dat)

8k9z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8k9z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.51 Å
Rg (electron density)	26.64 Å
Total Rg	27.35 Å
Atom count	4390
Residues	550
Excluded volume	77359 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8k9z__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8k9z__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RDTND-RID CBD
Molecular weight formula_weight	45959.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8608

ESLVAARAEKVANLYRWLDTDNDVATDKYVPVPGFERVDVDVSDEVKQRMIQSMSGYIEHTDNQVPKDQAEALATLFVESTLDYDWDKRVEFLTKLESYGYSFEAPHAEKSIVSFWSGKNFKQYRDILDNAQTDGKKVVYDIDVKGNAFAIDLNKHLMRWGGLFLDPDNAEQNQLKSSIDAATFSNTGFWSSVYATGAQNDVYVIAEGGVRLGNYFWNVELPALRQLQREGLVGEIRLLDKPVSEYKDLPADQIGRRLTDAGVAVKVRFDALSHERQAELLADNPDGYKADTLVELDVKLSAIDSMLRESLPFYSLRTERNLLVQEGEEGFEVRSWPGIDGKSKTILLDNPEDAAQQKSIERFILANFDNFEQMPDELFLVDNKVLSHHDGRTRIIAQKEDGAWT

Source Source

Source organism organism	Vibrio vulnificus
NCBI taxonomy ID ncbi_taxonomy_id	672
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calmodulin-2
Molecular weight formula_weight	16979.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GAMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDQMIREADIDGDGQVNYEEFVQMMTAK

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

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

▶

Unit-cell length a length_a	243.374 Å
Unit-cell length b length_b	49.778 Å
Unit-cell length c length_c	135.746 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	48.510 Å
R factor r_factor	0.2670
R_work r_work	0.2651
R_free r_free	0.3041

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin

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

RDTND-RID CBD

State in the Current Structure

Other States of the Same Protein in the Database

Calmodulin-2

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

8k9z__assembly_1__model_1

8k9z__assembly_1__model_1 | I(q)

8k9z__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 (4)

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 water

7. Citations (1)

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin

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

RDTND-RID CBD

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-2

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

8k9z__assembly_1__model_1

8k9z__assembly_1__model_1 | I(q)

8k9z__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 (4)

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 water

7. Citations (1)