SAXSdb — 9x9b

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1. Structure Basics

entry_id	9x9b
deposition_date	2025-10-20
title	Retron-Eco8 complex with ATP-Mg2+
keywords	complex, RNA BINDING PROTEIN/RNA/DNA, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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	63.99 Å
rg_electron	61.71 Å
i0	7388310000.00
molecular_weight	652450.0 kDa
excluded_volume	785560 Å³
envelope_volume	1261700 Å³
shell_volume	163380 Å³
envelope_diameter	231.3 Å
shell_rg	67.43 Å
envelope_rg	61.17 Å
shape_rg	61.60 Å
total_rg	62.16 Å
total_atoms	87061
n_residues	4869
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	216.6 Å
rg_real	63.81 Å
rg_real_error	2.20 Å
i0_real	7.3880e+09
i0_real_error	1.6790e+08
rg_reciprocal	64.12 Å
i0_reciprocal	7392000000.0000
total_estimate	0.8011
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	78.0 Å
skewness	0.295
kurtosis	-0.320
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0000
highest_alpha	921700000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Retron Eco8 reverse transcriptase
formula_weight	43273.2 kDa
ec_number	2.7.7.49
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,E,I,M
atom_count	87061

MKTKKMILVDKVFYEKILSVESFKENIITQSAIPKISNKEVRLISSGSKIFYAINNTSPHSHVQLRLNRFFLSHIPLNSAAKAFVRGGSYLKYLEPHIYGSSYCRLDISSFFNNISFDDVKQSLSPYIKDEYLIGTEQKLIDAILNSVGYESPIRKDKGMIIPMGFRTSPAISNIVFRKMDLLIQDFCAKKGVIYSRYADDMLFSNPRESKLLMSDYFIDEISSLLSIMGFNINQSKYISREKEISINGYVIENKGGNGSIGTIRLSKSKLNTVLKVTHALAQNIPYKNICNKYIKVRLKEKNIKYESKKDEFEKKYYRDQLINYLGGYRSYLISLVKFHSEYKCVNSDFIIQINGILNDIQNHIQKIKKNRRL

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Retron Eco8 OLD nuclease
formula_weight	87373.8 kDa
ec_number	3.1.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,F,J,N

MTIESIRVKNLLSFDDVILRDFRDINCIIGRNNVGKSNLLKVIRYFYAKLENKKVIPLDFHTNYNAVGEITFTFDTTRIKKIVTSRKNNGRFHKHIYNTLFKSSSVKLNFEELIARKNSTNKSFFSLTLTICKDDSVMWSVDDPKVRSLLATLYPFLYIETRHIDLYDWNPIWKLISNLNSFNFDDVDHDELVNFLDEKISSRKGDYKKYIDRVVSVIDTKPYTYKEKVINYIKVAIKGDSFVNAGEELFTQSDGTNSNKFLETLLHLLITLTRTEFISPIVYIDEPEVGLHPKLAESFVSNLNKIYSKFKKTSELSGPGRYKTPYPNIFYSTHSPSILKQTIKLFGKDQQVLHFSKKKDGSTRVNKINSTYSDERFLNIFSDNEARLFFSEYIVFVEGATELELFRNLSLLNLYPAFSLADIYDANEVILANINPGYSKASIPFVIIKDIDTLIDYSIKTEKFSLRPLFEKMIKELTKEFDYYDTGFGRVRKEIDLFSDIQSSTKKHMDSGLFFKRFSLHNLSSRINKVSRKLNRYFMTTTIEGALINEQSLPYFFNWIGDVILTQMTINNPNPDKFIEAMRRRYNIKSQVVPLFKSVFCIGLNHPVYSSAVDKQALRIKLSFLNYLKRKVYSDFNNEKEIVLALRLAFGGKTETQYTLDKLRKDGEAELFREKIKNYKNNELFFLEPQMTKTSGWVTTFLNYTIEKITSEESDDDRIRQKLSFIFPEIISIIEQASSSIEAEESSLTG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	RNA (82-MER)
formula_weight	26291.6 kDa
src_method	man
entity_count	4

Polymer

type	polyribonucleotide
strand_id	C,G,K,O

AAGCUUCUUCUUCGAUAGAAGCUGAGGAGUCCAGUUUGACUGGAUAAGGUGUUCGCCAUCUCUAGCCUCAGUAAAAACUAGC

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	DNA (83-MER)
formula_weight	25594.4 kDa
src_method	man
entity_count	4

Polymer

type	polydeoxyribonucleotide
strand_id	D,H,L,P

CAAGACCAATCTTTACACTCTGTGAGTATTAAAGTTACCTATAGCGCCAAGTGCGCAAAGGATGAGCTAGTTTTTTAGTTTTT

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 5 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

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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	2.80 Å
resolution_method	—
num_particles	123608

fit	/app/data/saxs_computation/x9/9x9b/9x9b.fit
pddf	/app/data/pr_computation/x9/9x9b/9x9b.pr.out
profile	/app/data/saxs_computation/x9/9x9b/9x9b.dat

Retron-Eco8 complex with ATP-Mg2+

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)