SAXSdb — 9vhl

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1. Structure Basics

entry_id	9vhl
deposition_date	2025-06-17
title	cryoEM structure of retron-Eco7 complex (form II)
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	46.24 Å
rg_electron	45.84 Å
i0	1281490000.00
molecular_weight	272500.0 kDa
excluded_volume	330860 Å³
envelope_volume	457700 Å³
shell_volume	82774 Å³
envelope_diameter	151.7 Å
shell_rg	51.01 Å
envelope_rg	44.96 Å
shape_rg	45.82 Å
total_rg	46.10 Å
total_atoms	19055
n_residues	2176
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	152.8 Å
rg_real	46.17 Å
rg_real_error	1.24 Å
i0_real	1.2810e+09
i0_real_error	2.3890e+07
rg_reciprocal	46.24 Å
i0_reciprocal	1282000000.0000
total_estimate	0.8948
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.4 Å
skewness	0.260
kurtosis	-0.573
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	165900000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.937

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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	19055

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	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 5 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 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	2.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.60 Å
resolution_method	—
num_particles	291980

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

cryoEM structure of retron-Eco7 complex (form II)

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)