SAXSdb — 9y4s

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

DNA integrity scanning protein DisA

Mycobacterium tuberculosis H37Rv

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 homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 5–356 Chain B； UniProt 5–356 Chain C； UniProt 5–356 Chain D； UniProt 5–356 Chain E； UniProt 5–356 Chain F； UniProt 5–356 Chain G； UniProt 5–356 Chain H； UniProt 5–356	Fragment：T5-S356	CL CHLORIDE ION × 14 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 2BA (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Morpheus Fusion F12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D-Glucosamine. MytuD.17706.a.B2.PW39404 at 13.1 mg/mL. Screened as apo protein but cyclic di-AMP was bound to 4 sites likely acquired from the expression host. plate 19976 F12 drop 2, Puck: PSL-2416, Cryo: direct	Resolution 2.89 Å R-free 0.252

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 9Y4S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Y9Y Crystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide Deposited 2025-09-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 5–356（352 aa） Fragment：T5-S356 Chain B 5–356（352 aa） Fragment：T5-S356 Chain C 5–356（352 aa） Fragment：T5-S356 Chain D 5–356（352 aa） Fragment：T5-S356 Chain E 5–356（352 aa） Fragment：T5-S356 Chain F 5–356（352 aa） Fragment：T5-S356 Chain G 5–356（352 aa） Fragment：T5-S356 Chain H 5–356（352 aa） Fragment：T5-S356	Not recorded	2BA (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide × 4 BR BROMIDE ION × 8 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. MytuD.17706.a.B2.PW39404 at 13.1 mg/mL. Screened as apo protein but cyclic di-AMP was bound to 4 sites likely acquired from the expression host. Larged ion modeled as a bromide was near each ligand. plate 19967 C12 drop 3, Puck: PSL-1611, Cryo: direct	Resolution 3.03 Å R-free 0.268

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DISA_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–360； UniProt 5–356 Author chain B； PDBConstruct 9–360； UniProt 5–356 Author chain C； PDBConstruct 9–360； UniProt 5–356 Author chain D； PDBConstruct 9–360； UniProt 5–356 Author chain E； PDBConstruct 9–360； UniProt 5–356 Author chain F； PDBConstruct 9–360； UniProt 5–356 Author chain G； PDBConstruct 9–360； UniProt 5–356 Author chain H； PDBConstruct 9–360； UniProt 5–356

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	9y4s
Deposition date deposition_date	2025-09-03
最后修订 last_revision	2025-09-17
Structure title title	Crystal structure of DNA integrity scanning protein (DisA) from Mycobacterium tuberculosis in complex with cyclic di-AMP
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, DisA; TRANSFERASE
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	51.45 Å
Radius of gyration Rg (electron density) rg_electron	51.99 Å
Forward intensity I(0) i0	1334150000.00
Molecular weight molecular_weight	289700.0 kDa
Excluded volume excluded_volume	358180 Å³
Envelope volume envelope_volume	531570 Å³
Hydration-shell volume shell_volume	88589 Å³
Envelope diameter envelope_diameter	181.4 Å
Shell Rg shell_rg	50.75 Å
Envelope Rg envelope_rg	52.35 Å
Shape Rg shape_rg	52.09 Å
Total Rg total_rg	51.61 Å
Total atoms total_atoms	20342
Residues n_residues	2678
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	187.3 Å
Rg (real space) rg_real	51.76 Å
Rg uncertainty (real space) rg_real_error	2.26 Å
I(0) (real space) i0_real	1.3340e+09
I(0) uncertainty (real space) i0_real_error	3.0200e+07
Rg (reciprocal space) rg_reciprocal	51.20 Å
I(0) (reciprocal space) i0_reciprocal	1333000000.0000
Solution quality estimate total_estimate	0.7970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	54.4 Å
Skewness Skewness skewness	0.643
Kurtosis Kurtosis kurtosis	0.030
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	139900000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.552; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.786

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA integrity scanning protein DisA
Molecular weight formula_weight	39426.5 kDa
EC 编号 ec_number	2.7.7.85
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	20342

MAHHHHHHTRPTLREAVARLAPGTGLRDGLERILRGRTGALIVLGHDENVEAICDGGFSLDVRYAATRLRELCKMDGAVVLSTDGSRIVRANVQLVPDPSIPTDESGTRHRSAERAAIQTGYPVISVSHSMNIVTVYVRGERHVLTDSATILSRANQAIATLERYKTRLDEVSRQLSRAEIEDFVTLRDVMTVVQRLELVRRIGLVIDYDVVELGTDGRQLRLQLDELLGGNDTARELIVRDYHANPEPPSTGQINATLDELDALSDGDLLDFTALAKVFGYPTTTEAQDSTLSPRGYRAMAGIPRLQFAHADLLVRAFGTLQGLLAASAGDLQSVDGIGAMWARHVREGLSQLAESTIS

来源 Source

来源生物 organism	Mycobacterium tuberculosis H37Rv
NCBI Class编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide ;
Molecular weight formula_weight	658.4 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	277.526 Å
Unit-cell length b length_b	74.263 Å
Unit-cell length c length_c	199.413 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	126.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

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

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	49.220 Å
R factor r_factor	0.2053
R_work r_work	0.2028
R_free r_free	0.2522

fit	/app/data/saxs_computation/y4/9y4s/9y4s.fit
pddf	/app/data/pr_computation/y4/9y4s/9y4s.pr.out
profile	/app/data/saxs_computation/y4/9y4s/9y4s.dat

Crystal structure of DNA integrity scanning protein (DisA) from Mycobacterium tuberculosis in complex with cyclic di-AMP

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

DNA integrity scanning protein DisA

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