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9qh3

Pseudomonas aeruginosa polynucleotide phosphorylase in complex with recognition site of RNase E

Method: ELECTRON MICROSCOPY D_max: 110.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qh3
deposition_date	2025-03-14
title	Pseudomonas aeruginosa 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	37.31 Å
rg_electron	36.50 Å
i0	511697000.00
molecular_weight	181810.0 kDa
excluded_volume	227140 Å³
envelope_volume	312910 Å³
shell_volume	68537 Å³
envelope_diameter	118.3 Å
shell_rg	45.58 Å
envelope_rg	35.28 Å
shape_rg	36.49 Å
total_rg	37.08 Å
total_atoms	25591
n_residues	1684
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	37.00 Å
rg_real_error	0.64 Å
i0_real	5.1170e+08
i0_real_error	8.6600e+06
rg_reciprocal	37.20 Å
i0_reciprocal	511800000.0000
total_estimate	0.9073
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	52.8 Å
skewness	-0.012
kurtosis	-0.642
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	131600000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Polyribonucleotide nucleotidyltransferase
formula_weight	59727.9 kDa
ec_number	2.7.7.8
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	25636

MNPVTKQFQFGQSTVTLETGRIARQATGAVLVTMDDVSVLVTVVGAKSPAEGRDFFPLSVHYQEKTYAAGRIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPEGFMNEVQVVCTVVSTNKKSDPDIAAMIGTSAALAISGIPFAGPIGAARVGFHPEIGYILNPTYEQLQSSSLDMVVAGTEDAVLMVESEADELTEDQMLGAVLFAHDEFQAVIRAVKELAAEAGKPAWDWKAPAENTVLVNAIKAELGEAISQAYTITIKQDRYNRLGELRDQAVALFAGEEEGKFPASEVKDVFGLLEYRTVRENIVNGKPRIDGRDTRTVRPLRIEVGVLGKTHGSALFTRGETQALVVATLGTARDAQLLDTLEGERKDAFMLHYNFPPFSVGECGRMGSPGRREIGHGRLARRGVAAMLPTQDEFPYTIRVVSEITESNGSSSMASVCGASLALMDAGVPVKAPVAGIAMGLVKEGEKFAVLTDILGDEDHLGDMDFKVAGTDKGVTALQMDIKINGITEEIMEIALGQALEARLNILGQMNQVIAKPRAELSENAP

Source

organism	Pseudomonas aeruginosa PAO1
ncbi_taxonomy_id	208964
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Ribonuclease E
formula_weight	2911.3 kDa
ec_number	3.1.26.12
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

VPANATGRALNDPREKRRLQREAER

Source

organism	Pseudomonas aeruginosa PAO1
ncbi_taxonomy_id	208964
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	ADENOSINE-5'-MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	45

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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	2.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	95237

fit	/app/data/saxs_computation/qh/9qh3/9qh3.fit
pddf	/app/data/pr_computation/qh/9qh3/9qh3.pr.out
profile	/app/data/saxs_computation/qh/9qh3/9qh3.dat

Pseudomonas aeruginosa 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 (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)