SAXSdb — 9wmh

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1. Structure Basics

entry_id	9wmh
deposition_date	2025-09-03
title	Cryo-EM strucutre of MbpAgo-gDNA-tgRNA complex
keywords	Mucilaginibacter paludis Argonaute with guide DNA, RNA BINDING PROTEIN/DNA/RNA, RNA BINDING PROTEIN-DNA-RNA complex; RNA BINDING PROTEIN/DNA/RNA
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	28.84 Å
rg_electron	28.54 Å
i0	160332000.00
molecular_weight	97081.0 kDa
excluded_volume	119910 Å³
envelope_volume	143790 Å³
shell_volume	40891 Å³
envelope_diameter	106.4 Å
shell_rg	36.74 Å
envelope_rg	28.79 Å
shape_rg	28.57 Å
total_rg	29.16 Å
total_atoms	6809
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	101.6 Å
rg_real	28.78 Å
rg_real_error	0.78 Å
i0_real	1.6030e+08
i0_real_error	2.3670e+06
rg_reciprocal	28.81 Å
i0_reciprocal	160300000.0000
total_estimate	0.8535
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.1 Å
skewness	0.330
kurtosis	-0.213
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	36850000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Piwi domain-containing protein
formula_weight	93827.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6809

HHHHHHSSGENLYFQGMKDHILNLYRIDNLSELDFSYKLIDFDLSFIAGKEELLNKQLQKIAEEVSSVTKGPTAVLKRNQRFFVAVPADKQMEDRSIDGIPFSIPIKLLPEVYRIDSKDIQGHQLDVVYKFLDYEIRRQLGQHRDLWKLNTHQFFLREPMKGIQGSINVFEGFTYKLARLADGHFYVTLDLSTKYIDKYCLSHYINEGNVRTFENNYKGRRFLYLNGDNWYTIELLGFGKSVKEQDFIREGTTYNVLNYITEKIEHSRTDLKRYVKPNDLSMSYTYPGRTMDPHSGATSLARMLYNTKDERVKSLHYLSIKGPSKRFEAINNYISSYFKNLKFNAGKLLISNEPLVEKIKNFWIPELLFNNNRRLKITGFNSGMRDFAYQRKQLIKNNGVLNRTSFDVQYLLVPDEQYMDANLVEGFKNNAEFLIKKLAPAFDKFIIIRYPVKSCTSASVQIQEIEKVLHRRNALHGFALVVLPDLDAFSPAFLKTFHELLKSKFYPDLKVQCASAHNISSFFKPFSTAGNNGIVEYRVVEALKGRFSSYLFYLVLEHLIVNRKWPYALAKNLFYDIYIGIDVHDRHAGFTFFFKNGEQIIFHPEEVPQKTNSQRVEKVRAKTLNKVIYEKLKLYIPLFAPNPNGIVIVRDGRSFGVEYKALQAAINTLAAEGIVNKDTVKYGVVDLHKQSSVPIRIAAKTNSYDQLENPVAGSYKLVSPKEGFIFSTGYPFDIKGTSRPLNLSMKEGDLDFMKVMEDVFCQIMLAFSAPDKSNFLPVIIKLIDTLLEPLTATRETADEAEEDEEEMMDIN

Source

organism	Mucilaginibacter paludis DSM 18603
ncbi_taxonomy_id	714943
host_organism	Escherichia coli

Entity 2 polymer

description	Guide DNA
formula_weight	5641.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

TGAGGTAGTAGGTTGTAT

Entity 3 polymer

description	Target RNA
formula_weight	5926.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

AUACAACCUACUACCUCAU

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

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6. Citations (1)

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resolution	2.55 Å
resolution_method	—
num_particles	1175425

fit	/app/data/saxs_computation/wm/9wmh/9wmh.fit
pddf	/app/data/pr_computation/wm/9wmh/9wmh.pr.out
profile	/app/data/saxs_computation/wm/9wmh/9wmh.dat

Cryo-EM strucutre of MbpAgo-gDNA-tgRNA complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)