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9ubo

The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5

Method: ELECTRON MICROSCOPY D_max: 199.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ubo
deposition_date	2025-04-03
title	The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5
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	61.27 Å
rg_electron	61.55 Å
i0	2399000000.00
molecular_weight	398850.0 kDa
excluded_volume	494680 Å³
envelope_volume	701510 Å³
shell_volume	103060 Å³
envelope_diameter	210.0 Å
shell_rg	56.07 Å
envelope_rg	62.18 Å
shape_rg	61.55 Å
total_rg	61.41 Å
total_atoms	28114
n_residues	3531
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	199.1 Å
rg_real	61.76 Å
rg_real_error	2.12 Å
i0_real	2.3990e+09
i0_real_error	5.4750e+07
rg_reciprocal	60.81 Å
i0_reciprocal	2395000000.0000
total_estimate	0.8262
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.3 Å
skewness	0.489
kurtosis	-0.387
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	94050000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.146

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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	A,D,B,C,E,F
atom_count	28114

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	man
entity_count	3

Polymer

type	polyribonucleotide
strand_id	X,Y,Z

AAAAAA

Source

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

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	2.840 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.84 Å
resolution_method	—
num_particles	106481

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

The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5

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

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)