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9zid

Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 5

Method: ELECTRON MICROSCOPY D_max: 162.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zid
deposition_date	2025-12-03
title	Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 5
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	47.10 Å
rg_electron	47.40 Å
i0	934968000.00
molecular_weight	149920.0 kDa
excluded_volume	144060 Å³
envelope_volume	260390 Å³
shell_volume	49849 Å³
envelope_diameter	169.8 Å
shell_rg	46.68 Å
envelope_rg	46.43 Å
shape_rg	47.38 Å
total_rg	47.40 Å
total_atoms	9938
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	162.3 Å
rg_real	47.49 Å
rg_real_error	1.60 Å
i0_real	9.3500e+08
i0_real_error	1.9050e+07
rg_reciprocal	47.10 Å
i0_reciprocal	934500000.0000
total_estimate	0.8488
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.3 Å
skewness	0.463
kurtosis	-0.417
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	26940000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.632

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	9939

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	29

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	998359

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

Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 5

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)