SAXSdb — 9xyi

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1. Structure Basics

entry_id	9xyi
deposition_date	2025-08-26
title	hPNPase RNA loading state
keywords	RNase, Protein-RNA Complex, RNA degradation, mitochondria, phosphorolytic enzyme, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	36.82 Å
rg_electron	36.06 Å
i0	637188000.00
molecular_weight	206460.0 kDa
excluded_volume	259260 Å³
envelope_volume	336620 Å³
shell_volume	72939 Å³
envelope_diameter	103.6 Å
shell_rg	46.00 Å
envelope_rg	35.19 Å
shape_rg	36.06 Å
total_rg	36.69 Å
total_atoms	14493
n_residues	1877
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	103.9 Å
rg_real	36.48 Å
rg_real_error	0.44 Å
i0_real	6.3720e+08
i0_real_error	9.1140e+06
rg_reciprocal	36.70 Å
i0_reciprocal	637300000.0000
total_estimate	0.8373
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.7 Å
skewness	-0.040
kurtosis	-0.648
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	191100000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Polyribonucleotide nucleotidyltransferase 1, mitochondrial
formula_weight	84417.1 kDa
ec_number	2.7.7.8
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	14493

MAVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYTHKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETFSVFAPTPSAMHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLLHNTQLDQRKIKHPTALGLEVGQEIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRSSIVMGEPISQSSSNSQSGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	;RNA (5'-R(PAPAPUPCPUPA)-3') ;
formula_weight	18647.3 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D

CACAACACACACCACACACACAUAAAACAAAACAGCUACGCCAUCCUCCCCCCAAUCUA

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

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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	2.460 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.46 Å
resolution_method	—
num_particles	162591

fit	/app/data/saxs_computation/xy/9xyi/9xyi.fit
pddf	/app/data/pr_computation/xy/9xyi/9xyi.pr.out
profile	/app/data/saxs_computation/xy/9xyi/9xyi.dat

hPNPase RNA loading state

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

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)