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9ubm

The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 4

Method: ELECTRON MICROSCOPY D_max: 194.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ubm
deposition_date	2025-04-03
title	The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 4
keywords	deaminase, complex, ATP, HYDROLASE/RNA, HYDROLASE-RNA complex; HYDROLASE/RNA
method	ELECTRON MICROSCOPY

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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	54.98 Å
rg_electron	55.08 Å
i0	1757340000.00
molecular_weight	340320.0 kDa
excluded_volume	422130 Å³
envelope_volume	588260 Å³
shell_volume	93429 Å³
envelope_diameter	207.8 Å
shell_rg	54.33 Å
envelope_rg	55.81 Å
shape_rg	55.07 Å
total_rg	55.10 Å
total_atoms	23994
n_residues	3027
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	194.1 Å
rg_real	55.36 Å
rg_real_error	2.22 Å
i0_real	1.7570e+09
i0_real_error	3.3220e+07
rg_reciprocal	54.66 Å
i0_reciprocal	1756000000.0000
total_estimate	0.8218
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.2 Å
skewness	0.596
kurtosis	-0.027
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	93470000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.735

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	adenosine deaminase
formula_weight	70328.0 kDa
ec_number	3.5.4.4
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	E,F,A,B,C,D
atom_count	23994

MRILLCSVGTSWAVVPEAMQLLGSQGFDEVHVLTTASSKISPGVEQLLRYFEMHPGPRFSISRVQDFEDLRSEQDHMLFEEVLWRWLLQRAPQAAHRYICLAGGYKTISAAMQRAAALFGACEVFHVLCEPRFGPQGNREASTLEEVEQAIATNALRFVRLGPEPGWPQLRLLSAPSFPLESTLQGPVHWVRASDMRLRQHVEGVLERSRHILAAWEGISELPIPALAAWPPSHLRWLHEPLDPVQDKAWVQALPKVELHCHLGGFATHGELLHKVRQEAANPESLPPVRAIPLPPGWPIPEEPIGLERYMRLGDNNGSALLKDPGCLRAQCRLLYEALLADHVAYAEIRCSPANYASASRSPWVVLQEIRNHFQQAMEETPEDRRCHVNLLLTATREEGGDRSRIARHLALAITAAEHWKNGCRVVGVDLAGFEDRTTRAAMFATDFEPVHRVGLAVTVHAGENDDVEGIWQAVFKLSARRLGHALHLSRSPDLLRVVAERGIAVELCPYANLQIKGFPLDEEQEGSETYPLRGYLAAGVAVTLNTDNLGISQASLTDNLLLTARLCPGITRLEVLKTQVFAAQAAFANQAERKALWARLAQVPVPTDTEQKNGNDAKASHQPRHHHHHH

Source

organism	Thermoanaerobaculum aquaticum
ncbi_taxonomy_id	1312852
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	;RNA (5'-R(PAPAPAPAPAPA)-3') ;
formula_weight	1930.3 kDa
src_method	syn
entity_count	2

Polymer

type	polyribonucleotide
strand_id	X,Y

AAAAAA

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.940 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.94 Å
resolution_method	—
num_particles	80058

fit	/app/data/saxs_computation/ub/9ubm/9ubm.fit
pddf	/app/data/pr_computation/ub/9ubm/9ubm.pr.out
profile	/app/data/saxs_computation/ub/9ubm/9ubm.dat

The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 4

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)