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9qh0

Escherichia coli polynucleotide phosphorylase in complex with recognition site of RNase E

Method: ELECTRON MICROSCOPY D_max: 108.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qh0
deposition_date	2025-03-14
title	Escherichia coli polynucleotide phosphorylase in complex with recognition site of RNase E
keywords	polynucleotide phosphorylase, ribonuclease E, RNA degradosome, 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	37.64 Å
rg_electron	36.63 Å
i0	528104000.00
molecular_weight	184300.0 kDa
excluded_volume	229990 Å³
envelope_volume	315360 Å³
shell_volume	68608 Å³
envelope_diameter	111.1 Å
shell_rg	45.88 Å
envelope_rg	35.35 Å
shape_rg	36.63 Å
total_rg	37.23 Å
total_atoms	12939
n_residues	1702
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	108.2 Å
rg_real	37.30 Å
rg_real_error	0.55 Å
i0_real	5.2810e+08
i0_real_error	7.9530e+06
rg_reciprocal	37.51 Å
i0_reciprocal	528200000.0000
total_estimate	0.8382
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.1 Å
skewness	-0.046
kurtosis	-0.692
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	138600000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; 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
formula_weight	59656.8 kDa
ec_number	2.7.7.8
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	12946

MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNEALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAPRGDIS

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Ribonuclease E
formula_weight	6147.7 kDa
ec_number	3.1.26.12
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

NHATAPMTRAPAPEYVPEAPRHSDWQRPTFAFEGKGAAGGHTATHHASAAPARPQPVE

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	7

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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	2.520 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.52 Å
resolution_method	—
num_particles	108374

fit	/app/data/saxs_computation/qh/9qh0/9qh0.fit
pddf	/app/data/pr_computation/qh/9qh0/9qh0.pr.out
profile	/app/data/saxs_computation/qh/9qh0/9qh0.dat

Escherichia coli polynucleotide phosphorylase in complex with recognition site of RNase E

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)