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9y4s

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

Method: X-RAY DIFFRACTION D_max: 187.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y4s
deposition_date	2025-09-03
last_revision	2025-09-17
title	Crystal structure of DNA integrity scanning protein (DisA) from Mycobacterium tuberculosis in complex with cyclic di-AMP
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, DisA; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	51.45 Å
rg_electron	51.99 Å
i0	1334150000.00
molecular_weight	289700.0 kDa
excluded_volume	358180 Å³
envelope_volume	531570 Å³
shell_volume	88589 Å³
envelope_diameter	181.4 Å
shell_rg	50.75 Å
envelope_rg	52.35 Å
shape_rg	52.09 Å
total_rg	51.61 Å
total_atoms	20342
n_residues	2678
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	187.3 Å
rg_real	51.76 Å
rg_real_error	2.26 Å
i0_real	1.3340e+09
i0_real_error	3.0200e+07
rg_reciprocal	51.20 Å
i0_reciprocal	1333000000.0000
total_estimate	0.7970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	54.4 Å
skewness	0.643
kurtosis	0.030
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	139900000.0000
n_real_points	32
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DNA integrity scanning protein DisA
formula_weight	39426.5 kDa
ec_number	2.7.7.85
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	20342

MAHHHHHHTRPTLREAVARLAPGTGLRDGLERILRGRTGALIVLGHDENVEAICDGGFSLDVRYAATRLRELCKMDGAVVLSTDGSRIVRANVQLVPDPSIPTDESGTRHRSAERAAIQTGYPVISVSHSMNIVTVYVRGERHVLTDSATILSRANQAIATLERYKTRLDEVSRQLSRAEIEDFVTLRDVMTVVQRLELVRRIGLVIDYDVVELGTDGRQLRLQLDELLGGNDTARELIVRDYHANPEPPSTGQINATLDELDALSDGDLLDFTALAKVFGYPTTTEAQDSTLSPRGYRAMAGIPRLQFAHADLLVRAFGTLQGLLAASAGDLQSVDGIGAMWARHVREGLSQLAESTIS

Source

organism	Mycobacterium tuberculosis H37Rv
ncbi_taxonomy_id	83332
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	14

Entity 3 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

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 ;
formula_weight	658.4 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	277.526 Å
length_b	74.263 Å
length_c	199.413 Å
angle_alpha	90.00 °
angle_beta	126.05 °
angle_gamma	90.00 °
z_pdb	32

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.890 Å
resolution_low	49.220 Å
r_factor	0.2053
r_work	0.2028
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