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9v66

Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA

Method: ELECTRON MICROSCOPY D_max: 94.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v66
deposition_date	2025-05-26
title	Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA
keywords	mesophilic prokaryotic Argonaute, RNA BINDING PROTEIN/DNA, RNA BINDING PROTEIN-DNA complex; RNA BINDING PROTEIN/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	30.17 Å
rg_electron	29.37 Å
i0	148129000.00
molecular_weight	91704.0 kDa
excluded_volume	112990 Å³
envelope_volume	148890 Å³
shell_volume	41614 Å³
envelope_diameter	94.6 Å
shell_rg	37.29 Å
envelope_rg	29.03 Å
shape_rg	29.36 Å
total_rg	30.09 Å
total_atoms	6448
n_residues	778
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	94.6 Å
rg_real	30.02 Å
rg_real_error	0.53 Å
i0_real	1.4810e+08
i0_real_error	2.0810e+06
rg_reciprocal	30.09 Å
i0_reciprocal	148100000.0000
total_estimate	0.9015
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.5 Å
skewness	0.185
kurtosis	-0.470
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	39490000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.959

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	VbAgo
formula_weight	88463.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6456

MSEKQLGATLFPITGLPAQAFRLRVLRVRETIPMDTQTPVRLNRWATQLWKELKQAVVPTGRFEWPAFLTPDVESLTVGRVLTVQDVPDREYSIEVIGETVEVNPASASSEELQLAGEMIKRAISDAFGRNSDKYWRKHWNLYFRLEPENLQDRRDRVFAYRGLKFSVVFLGDKPWLAADILTTYHGQHALSEYSSEQRQRELHFHVSERIEADDRAMFLRDNGKIKIPCRFVGSTGKTVTQYTFPINGGQKNVREYYEQRYGIRVPENDEAVFVRDREGCDSWPVPASRLFPLFTTEYDEVRNCSVVPQMPPDERVETIRAFLNDLRDVSFAGSTLAIGHSHFQTAERSVFPAPALEFGNGQTLTVDASLPIEEGYNRYRQGKMTMLYEHGPFSSQSLPDLVLLYPDNLDRNAREKLRQRLGEEIKELCGVAPRIARQISYPLGKQPHAGAGLLAAADELVRNNDGTFLPVIVLADALREHIYDLLKRRLSSLASQCVRERTVARVARDEQAVGGSRLRNLALGILTAAGLQPWVLAKPLHYDFYMGVDLLANQVIYVFVCGKGGRNVWVQRGDQLRRRGITEKIDRVQLADQFKTGVREAKRLGVPLNSLVVHRDGRWWSNEDLAITEAVAELQGDGTLSKDCQVGVVEVRKSHLPVRLFSVLNATKGSLENPMPGSHLILNNTEAILTPTGQPGRWDKQGRTAGTLLLRITRNPNGSPLDIRKIAEDAYGLTHLNWNAPDIEISLPVTIRWSDERLREIVTNPSATDDTEVEPQETCIV

Source

organism	Verrucomicrobiota bacterium
ncbi_taxonomy_id	2026799
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PTPGPAPGPGPTPAPGPTPAPGPGPTPTPGPTPAPT)-3') ;
formula_weight	5641.7 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

TGAGGTAGTAGGTTGTAT

Source

organism	Verrucomicrobiota bacterium
ncbi_taxonomy_id	2026799
host_organism	Escherichia coli

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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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	2.950 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.95 Å
resolution_method	—
num_particles	186978

fit	/app/data/saxs_computation/v6/9v66/9v66.fit
pddf	/app/data/pr_computation/v6/9v66/9v66.pr.out
profile	/app/data/saxs_computation/v6/9v66/9v66.dat

Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)