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9zix

Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 20

Method: ELECTRON MICROSCOPY D_max: 160.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zix
deposition_date	2025-12-04
title	Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 20
keywords	ribozyme, RNA, RNase P., RNA-Hydrolase complex; RNA/HYDROLASE
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	46.17 Å
rg_electron	46.50 Å
i0	934254000.00
molecular_weight	149800.0 kDa
excluded_volume	143960 Å³
envelope_volume	255100 Å³
shell_volume	49616 Å³
envelope_diameter	167.6 Å
shell_rg	46.24 Å
envelope_rg	45.55 Å
shape_rg	46.47 Å
total_rg	46.53 Å
total_atoms	9933
n_residues	533
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	160.5 Å
rg_real	46.54 Å
rg_real_error	2.38 Å
i0_real	9.3430e+08
i0_real_error	1.8170e+07
rg_reciprocal	46.17 Å
i0_reciprocal	933800000.0000
total_estimate	0.8493
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.5 Å
skewness	0.480
kurtosis	-0.308
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	28620000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.636

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNase P RNA (417-MER)
formula_weight	135305.2 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	9933

GUUAAUCAUGCUCGGGUAAUCGCUGCGGCCGGUUUCGGCCGUAGAGGAAAGUCCAUGCUCGCACGGUGCUGAGAUGCCCGUAGUGUUCGUGCCUAGCGAAUCCAUAAGCUAGGGCAGCCUGGCUUUGGCUGGGCUGACGGCGGGGAAAGAACCUACGUCCGGCUGGGAUAUGGUUCGAUUACCCUGAAAGUGCCACAGUGACGGAGCUCUAAGGGAAACCUUAGAGGUGGAACGCGGUAAACCCCACGAGCGAGAAACCCAAAUGAUGGUAGGGGCACCUUCCCGAAGGAAAUGAACGGAGGGAAGGACAGGCGGCGCAUGCAGCCUGUAGAUAGAUGAUUACCGCCGGAGUACGAGGCGCAAAGCCGCUUGCAGUACGAAGGUACAGAACAUGGCUUAUAGAGCAUGAUUAACGUC

Source

organism	Geobacillus stearothermophilus
ncbi_taxonomy_id	1422
host_organism	in vitro transcription vector pT7-TP(deltai)

Entity 2 polymer

description	Ribonuclease P protein component
formula_weight	13456.9 kDa
ec_number	3.1.26.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GMKKKYRIKKNEEFQEVFQQGVSVANRQFVVYTLDRPEQPYFRIGLSVSKKLGKAVVRNRIKRYIRQCFLELKEEVAPGKDYVIIARQPAAEMGYAEVKKSLIHVLRKAGGLKKEA

Source

organism	Geobacillus stearothermophilus
ncbi_taxonomy_id	1422
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	24

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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	3.680 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.68 Å
resolution_method	—
num_particles	31380

fit	/app/data/saxs_computation/zi/9zix/9zix.fit
pddf	/app/data/pr_computation/zi/9zix/9zix.pr.out
profile	/app/data/saxs_computation/zi/9zix/9zix.dat

Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 20

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)