SAXSdb — 9vhe

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1. Structure Basics

entry_id	9vhe
deposition_date	2025-06-16
title	cryoEM structure of retron-Eco7 complex
keywords	retron-Eco7, toxin-antitoxin, DNA BINDING PROTEIN/RNA/DNA, DNA BINDING PROTEIN-RNA-DNA complex; DNA 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	47.44 Å
rg_electron	47.35 Å
i0	1304280000.00
molecular_weight	274670.0 kDa
excluded_volume	333360 Å³
envelope_volume	465350 Å³
shell_volume	82627 Å³
envelope_diameter	167.4 Å
shell_rg	50.84 Å
envelope_rg	46.99 Å
shape_rg	47.33 Å
total_rg	47.53 Å
total_atoms	19207
n_residues	2195
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	159.0 Å
rg_real	47.58 Å
rg_real_error	1.23 Å
i0_real	1.3040e+09
i0_real_error	2.1860e+07
rg_reciprocal	47.44 Å
i0_reciprocal	1304000000.0000
total_estimate	0.8675
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.2 Å
skewness	0.418
kurtosis	-0.379
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0001
highest_alpha	171100000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.744

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Retron Ec78 reverse transcriptase
formula_weight	35629.2 kDa
ec_number	2.7.7.49
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	19207

MSVIRRLAAVLRQSDSGISAFLVTAPRKYKVYKIPKRTTGFRVIAQPAKGLKDIQRAFVQLYNFPVHDASMAYMKGKGIRDNAAAHAGNQYLLKADLEDFFNSITPAIFWRCIEMSSALTPQFEPQDKFFIEKILFWQPIKHRKTKLILSVGAPSSPVISNFCMYEFDNRIHAACNKLEITYTRYADDLTFSCNIPNVLKAVPSTIEALLKDLFGSELRLNHSKTVFSSKAHNRHVTGVTINNEETLSLGRDRKRFIKHLINQYKYGLLDNEDKAYLTGLLAFASHIEPGFITRMNEKYSLELMERLRGQR

Source

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

Entity 2 polymer

description	Retron Ec78 probable ATPase
formula_weight	62466.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,C,D,E

MTKQYERKAKGGNLLSAFELYQRNTDNMPGLGEMLVDEWFETCRDYIQDGHVDESGTFRPDNAFYLRRLTLKDFRRFSLLEIKFEEDLTVIIGNNGKGKTSILYAIAKTLSWFVANILKEGGSGQRLSELTDIKNDAENRYADVSSTFFFGKGLKSVPIRLSRSALGTAERRDSEVKPARDLADIWRVINEAKTINLPTFALYNVERSQPFNRNTKDNAGRREERFDAYSQALGGAGRFDHFVEWYIYLHKRTISDISSSIKELEQQVNDLQRSVDGGMVSVKSLLEQMKLKLSEASERNDAAVSSKMVTESVQKSIVEKSICSVVPSISKIWVEMTTGSDLVKVTNDGHDVTIDQLSDGQRVFLSLVADLARRMVMLNPLLENPLEGRGIVLIDEIELHLHPKWQQEVILNLRSVFPNIQFIITTHSPIVLSTIEKRCIREFDPNDDGNQSFLDSPDMQTKGSENAQILEQVMNVHPTPPGIAESHWLGDFELLLLDNSGELDNQSQELYDKIKTHFGIDSAELKKADSLIRINKMKNKINKIRAEKGK

Source

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

Entity 3 polymer

description	Retron Ec78 putative HNH endonuclease
formula_weight	24816.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MKELARLESPEILDQYTAGQNDWMEIDQSAVWPKLTEMQGEFCAYCECRLNRRHIEHFRPRGKFPALTFIWSNLFGSCGDSKKSGGWSRCGIYKDNGAGAYNADDLIKPDEENPDDYLLFLTTGEVVPAIGLTGRALKKAQETIRVFNLNGDIKLLGSRRTAVQAIMPNVEYLYSLLEEFEEDDWNEMLRDELEKIESDEFKTALKHAWTSNQEFA

Source

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

Entity 4 polymer

description	msrRNA
formula_weight	20813.3 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	H

ACUCUUUAGCGUUGGACGGUUACGUCUAGUCGGGUGAUUAGCCAGACUCUAACUUAUUGAACGUA

Source

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

Entity 5 polymer

description	msdDNA
formula_weight	22869.6 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	G

GGAAGCGAAAGTGTCGCAACCCGAGAGAGGAACGATCTCGGGTTGCGACACTTTCGCAACCCTTAATACGTTCA

Source

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

Entity 6 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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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	2.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.50 Å
resolution_method	—
num_particles	413082

fit	/app/data/saxs_computation/vh/9vhe/9vhe.fit
pddf	/app/data/pr_computation/vh/9vhe/9vhe.pr.out
profile	/app/data/saxs_computation/vh/9vhe/9vhe.dat

cryoEM structure of retron-Eco7 complex

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)