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9ypf

S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate

Method: ELECTRON MICROSCOPY D_max: 110.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ypf
deposition_date	2025-10-14
title	S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
keywords	exonuclease, translation, RNA, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/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	37.82 Å
rg_electron	36.63 Å
i0	553603000.00
molecular_weight	186860.0 kDa
excluded_volume	232070 Å³
envelope_volume	314190 Å³
shell_volume	68389 Å³
envelope_diameter	118.2 Å
shell_rg	45.41 Å
envelope_rg	35.70 Å
shape_rg	36.61 Å
total_rg	37.22 Å
total_atoms	13114
n_residues	1588
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	110.8 Å
rg_real	37.47 Å
rg_real_error	0.46 Å
i0_real	5.5360e+08
i0_real_error	6.8070e+06
rg_reciprocal	37.69 Å
i0_reciprocal	553700000.0000
total_estimate	0.8946
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.7 Å
skewness	-0.011
kurtosis	-0.522
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	107700000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.854

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cmp-binding-factor 1
formula_weight	35785.8 kDa
mutation	D193A
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	13114

MRNIENLNPGDSVDHFFLVHKATQGVTAQGKDYMTLHLQDKSGEIEAKFWTATKNDMATIKPEEIVHVKGDIINYRGNKQMKVNQIRLATTEDQLKTEQFVDGAPLSPAEIQEEISHYLLDIENANLQRITRHLLKKYQERFYTYPAASSHHHNFASGLSYHVLTMLRIAKSICDIYPLLNKSLLYSGIILHAIGKVRELSGPVATSYTVEGNLLGHISIASDEVVEAARELNIEGEEIMLLRHMILSHHGKLEYGSPKLPYLKEAEILCYIDNIDARMNMFEKAYKKTDKGQFTDKIFGLENRRFYNPESLD

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 polymer

description	RNA
formula_weight	12636.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	G

UAAAGCACUUGUGUUUUUGCACAAGUGCUUUUUUAUACUC

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	6

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6. Citations (1)

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resolution	3.50 Å
resolution_method	—
num_particles	42145

fit	/app/data/saxs_computation/yp/9ypf/9ypf.fit
pddf	/app/data/pr_computation/yp/9ypf/9ypf.pr.out
profile	/app/data/saxs_computation/yp/9ypf/9ypf.dat

S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate

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 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)