SAXSdb — 8ka2

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

RDTND-RID CBD

Vibrio vulnificus

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 1959–2374	Fragment：MARTX toxin DUF1-RIDcbd region Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；22% (w/v) PEG 3350 and 4% (v/v) Tacsimate (pH 6.0)	Resolution 3.38 Å R-free 0.322
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1959–2374	Fragment：MARTX toxin DUF1-RIDcbd region Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；22% (w/v) PEG 3350 and 4% (v/v) Tacsimate (pH 6.0)	Resolution 3.38 Å R-free 0.322

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.

Other PDB	Difference from Current Entry 8KA2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8K9Z 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 Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1967–2371（405 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG 3350 and 0.18 M magnesium acetate	Resolution 2.90 Å R-free 0.304
8K9Z 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 Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1967–2371（405 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG 3350 and 0.18 M magnesium acetate	Resolution 2.90 Å R-free 0.304
8KA0 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 and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1959–2374（416 aa） Fragment：DUF1-RIDcbd (residues, 1959-2374)	Mutation：E2186Q	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA0 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 and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1959–2374（416 aa） Fragment：DUF1-RIDcbd (residues, 1959-2374)	Mutation：E2186Q	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA0 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 and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1959–2374（416 aa） Fragment：DUF1-RIDcbd (residues, 1959-2374)	Mutation：E2186Q	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA0 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 and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1959–2374（416 aa） Fragment：DUF1-RIDcbd (residues, 1959-2374)	Mutation：E2186Q	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1959–2374（416 aa） Fragment：MARTX toxin DUF1-RIDcbd region	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1959–2374（416 aa） Fragment：MARTX toxin DUF1-RIDcbd region	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1959–2374（416 aa） Fragment：MARTX toxin DUF1-RIDcbd region	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1959–2374（416 aa） Fragment：MARTX toxin DUF1-RIDcbd region	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342

3 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MARTX_VIBVL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–419； UniProt 1959–2374 Author chain B； PDBConstruct 4–419； UniProt 1959–2374

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	8ka2
Deposition date deposition_date	2023-08-02
Structure title title	Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus
Keywords keywords	MARTX toxin, RDTND-RID, NADase, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	32.84 Å
Radius of gyration Rg (electron density) rg_electron	32.31 Å
Forward intensity I(0) i0	114027000.00
Molecular weight molecular_weight	83188.0 kDa
Excluded volume excluded_volume	103230 Å³
Envelope volume envelope_volume	138300 Å³
Hydration-shell volume shell_volume	36783 Å³
Envelope diameter envelope_diameter	123.0 Å
Shell Rg shell_rg	37.97 Å
Envelope Rg envelope_rg	32.33 Å
Shape Rg shape_rg	32.31 Å
Total Rg total_rg	32.78 Å
Total atoms total_atoms	5848
Residues n_residues	719
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.4 Å
Rg (real space) rg_real	32.95 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	1.1400e+08
I(0) uncertainty (real space) i0_real_error	2.0210e+06
Rg (reciprocal space) rg_reciprocal	32.90 Å
I(0) (reciprocal space) i0_reciprocal	114000000.0000
Solution quality estimate total_estimate	0.8656
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26970000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	207.726 Å
Unit-cell length b length_b	207.726 Å
Unit-cell length c length_c	54.647 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	3.380 Å
Low-resolution limit resolution_low	40.420 Å
R factor r_factor	0.2879
R_work r_work	0.2860
R_free r_free	0.3221

Description description	RDTND-RID CBD
Molecular weight formula_weight	47633.8 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5848

Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Vibrio vulnificus
通用名 common_name	DUF1-RIDcbd
NCBI Class编号 ncbi_taxonomy_id	672
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/ka/8ka2/8ka2.fit
pddf	/app/data/pr_computation/ka/8ka2/8ka2.pr.out
profile	/app/data/saxs_computation/ka/8ka2/8ka2.dat