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9vh1

cryoEM structure of ptuA-ptuB complex in Retron-Eco7 anti-phage system

Method: ELECTRON MICROSCOPY D_max: 84.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vh1
deposition_date	2025-06-16
last_revision	2025-12-03
title	cryoEM structure of ptuA-ptuB complex in Retron-Eco7 anti-phage system
keywords	retron-Eco7, toxin-antitoxin, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	27.07 Å
rg_electron	26.22 Å
i0	66314000.00
molecular_weight	64063.0 kDa
excluded_volume	80504 Å³
envelope_volume	100580 Å³
shell_volume	31797 Å³
envelope_diameter	89.6 Å
shell_rg	33.55 Å
envelope_rg	26.47 Å
shape_rg	26.21 Å
total_rg	27.04 Å
total_atoms	9004
n_residues	555
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	84.0 Å
rg_real	26.96 Å
rg_real_error	0.47 Å
i0_real	6.6310e+07
i0_real_error	9.0540e+05
rg_reciprocal	27.00 Å
i0_reciprocal	66320000.0000
total_estimate	0.9051
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.1 Å
skewness	0.212
kurtosis	-0.445
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	19500000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.929

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Retron Ec78 probable ATPase
formula_weight	62466.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,E
atom_count	9004

MTKQYERKAKGGNLLSAFELYQRNTDNMPGLGEMLVDEWFETCRDYIQDGHVDESGTFRPDNAFYLRRLTLKDFRRFSLLEIKFEEDLTVIIGNNGKGKTSILYAIAKTLSWFVANILKEGGSGQRLSELTDIKNDAENRYADVSSTFFFGKGLKSVPIRLSRSALGTAERRDSEVKPARDLADIWRVINEAKTINLPTFALYNVERSQPFNRNTKDNAGRREERFDAYSQALGGAGRFDHFVEWYIYLHKRTISDISSSIKELEQQVNDLQRSVDGGMVSVKSLLEQMKLKLSEASERNDAAVSSKMVTESVQKSIVEKSICSVVPSISKIWVEMTTGSDLVKVTNDGHDVTIDQLSDGQRVFLSLVADLARRMVMLNPLLENPLEGRGIVLIDEIELHLHPKWQQEVILNLRSVFPNIQFIITTHSPIVLSTIEKRCIREFDPNDDGNQSFLDSPDMQTKGSENAQILEQVMNVHPTPPGIAESHWLGDFELLLLDNSGELDNQSQELYDKIKTHFGIDSAELKKADSLIRINKMKNKINKIRAEKGK

Source

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

Entity 2 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 3 non-polymer

description	ZINC ION
formula_weight	65.4 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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	165087

fit	/app/data/saxs_computation/vh/9vh1/9vh1.fit
pddf	/app/data/pr_computation/vh/9vh1/9vh1.pr.out
profile	/app/data/saxs_computation/vh/9vh1/9vh1.dat

cryoEM structure of ptuA-ptuB complex in Retron-Eco7 anti-phage system

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)