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9pqv

Crystal structure of C. elegans PUF-3 in complex with RNA II-2

Method: X-RAY DIFFRACTION D_max: 110.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pqv
deposition_date	2025-07-23
title	Crystal structure of C. elegans PUF-3 in complex with RNA II-2
keywords	RNA binding, Caenorhabditis elegans, PUF protein, RNA BINDING PROTEIN; RNA BINDING PROTEIN
method	X-RAY DIFFRACTION

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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	30.18 Å
rg_electron	30.30 Å
i0	46978800.00
molecular_weight	50543.0 kDa
excluded_volume	61828 Å³
envelope_volume	84003 Å³
shell_volume	24574 Å³
envelope_diameter	117.4 Å
shell_rg	34.93 Å
envelope_rg	31.60 Å
shape_rg	30.34 Å
total_rg	30.62 Å
total_atoms	3527
n_residues	420
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	110.7 Å
rg_real	30.55 Å
rg_real_error	1.42 Å
i0_real	4.6980e+07
i0_real_error	8.5390e+05
rg_reciprocal	30.40 Å
i0_reciprocal	46970000.0000
total_estimate	0.7647
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.570
kurtosis	-0.326
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	8711000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.520; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.398; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PUM-HD domain-containing protein
formula_weight	47039.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3581

SAVRLIDLENNASFSKSLNSTTRSHKCTLPIWAGDGEGNVSDSVTLQDVLANDALVEFATDKNGCRFLQEHYPTENDNDVHQKLFRKLVEDRAIFLSLCSNMFGNFFVQRVLECSNTEEQEILTEHLATDLYNLCLDKSACRVIQLAIQKLDVHLATRLSLELRDTHLVRLSIDQNGNHVIQKIVKTLPVSSWTFLVDFFADDDNLIHVCQDKYGCRVIQSTVETLSTDQYAQCYQHRVILLRSLMAGVTRNCTQLASNEFANYVVQHVIKCGDALAVYRDIIIEQCLLQNLLSMSQEKYASHVVEVAFECAPYRLVAEMMNEIFEGYIPHPDTNRDALDILLFHQYGNYVVQQMIQTCVLGQNARDQKQSEMYGMWLEKIHGRVMRNAHRLERFSSGKKIIEALQSMSLY

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 2 polymer

description	RNA II-2
formula_weight	3122.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

CUGUACUAUA

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	4

Entity 4 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	nat
entity_count	13

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	33

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6. Citations (1)

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length_a	161.758 Å
length_b	161.758 Å
length_c	100.259 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.920 Å
resolution_low	29.240 Å
r_factor	0.1972
r_work	0.1961
r_free	0.2138

fit	/app/data/saxs_computation/pq/9pqv/9pqv.fit
pddf	/app/data/pr_computation/pq/9pqv/9pqv.pr.out
profile	/app/data/saxs_computation/pq/9pqv/9pqv.dat

Crystal structure of C. elegans PUF-3 in complex with RNA II-2

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

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)