SAXSdb — 9wmf

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1. Structure Basics

entry_id	9wmf
deposition_date	2025-09-03
title	Cryo-EM strucutre of MbpAgo-gDNA complex
keywords	Mucilaginibacter paludis Argonaute with guide DNA, 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	38.73 Å
rg_electron	38.35 Å
i0	487159000.00
molecular_weight	185040.0 kDa
excluded_volume	233670 Å³
envelope_volume	308240 Å³
shell_volume	65443 Å³
envelope_diameter	130.2 Å
shell_rg	45.43 Å
envelope_rg	38.04 Å
shape_rg	38.34 Å
total_rg	38.80 Å
total_atoms	13068
n_residues	1574
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	125.5 Å
rg_real	38.62 Å
rg_real_error	0.86 Å
i0_real	4.8720e+08
i0_real_error	8.3060e+06
rg_reciprocal	38.69 Å
i0_reciprocal	487200000.0000
total_estimate	0.8808
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.9 Å
skewness	0.311
kurtosis	-0.284
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	77200000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.853

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Piwi domain-containing protein
formula_weight	93827.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13068

HHHHHHSSGENLYFQGMKDHILNLYRIDNLSELDFSYKLIDFDLSFIAGKEELLNKQLQKIAEEVSSVTKGPTAVLKRNQRFFVAVPADKQMEDRSIDGIPFSIPIKLLPEVYRIDSKDIQGHQLDVVYKFLDYEIRRQLGQHRDLWKLNTHQFFLREPMKGIQGSINVFEGFTYKLARLADGHFYVTLDLSTKYIDKYCLSHYINEGNVRTFENNYKGRRFLYLNGDNWYTIELLGFGKSVKEQDFIREGTTYNVLNYITEKIEHSRTDLKRYVKPNDLSMSYTYPGRTMDPHSGATSLARMLYNTKDERVKSLHYLSIKGPSKRFEAINNYISSYFKNLKFNAGKLLISNEPLVEKIKNFWIPELLFNNNRRLKITGFNSGMRDFAYQRKQLIKNNGVLNRTSFDVQYLLVPDEQYMDANLVEGFKNNAEFLIKKLAPAFDKFIIIRYPVKSCTSASVQIQEIEKVLHRRNALHGFALVVLPDLDAFSPAFLKTFHELLKSKFYPDLKVQCASAHNISSFFKPFSTAGNNGIVEYRVVEALKGRFSSYLFYLVLEHLIVNRKWPYALAKNLFYDIYIGIDVHDRHAGFTFFFKNGEQIIFHPEEVPQKTNSQRVEKVRAKTLNKVIYEKLKLYIPLFAPNPNGIVIVRDGRSFGVEYKALQAAINTLAAEGIVNKDTVKYGVVDLHKQSSVPIRIAAKTNSYDQLENPVAGSYKLVSPKEGFIFSTGYPFDIKGTSRPLNLSMKEGDLDFMKVMEDVFCQIMLAFSAPDKSNFLPVIIKLIDTLLEPLTATRETADEAEEDEEEMMDIN

Source

organism	Mucilaginibacter paludis DSM 18603
ncbi_taxonomy_id	714943
host_organism	Escherichia coli

Entity 2 polymer

description	;guide DNA (5'-D(PT)-R(PGPAPGPG)-D(PT)-R(PAPG)-3') ;
formula_weight	5641.7 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,D

TGAGGTAGTAGGTTGTAT

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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	3.570 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.57 Å
resolution_method	—
num_particles	325973

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

Cryo-EM strucutre of MbpAgo-gDNA 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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)