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9ptj

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

Method: X-RAY DIFFRACTION D_max: 109.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ptj
deposition_date	2025-07-29
title	Crystal structure of C. elegans PUF-3 in complex with RNA II-3
keywords	RNA binding, Caenorhabditis elegans, PUF-3, 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	29.50 Å
rg_electron	29.66 Å
i0	46612200.00
molecular_weight	50006.0 kDa
excluded_volume	61007 Å³
envelope_volume	82541 Å³
shell_volume	24567 Å³
envelope_diameter	114.7 Å
shell_rg	34.57 Å
envelope_rg	31.05 Å
shape_rg	29.70 Å
total_rg	29.97 Å
total_atoms	3489
n_residues	422
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	109.9 Å
rg_real	29.83 Å
rg_real_error	1.29 Å
i0_real	4.6610e+07
i0_real_error	8.4860e+05
rg_reciprocal	29.69 Å
i0_reciprocal	46610000.0000
total_estimate	0.7710
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.586
kurtosis	-0.256
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	7126000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.526; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.485; Smooth: 0.957

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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	3509

SAVRLIDLENNASFSKSLNSTTRSHKCTLPIWAGDGEGNVSDSVTLQDVLANDALVEFATDKNGCRFLQEHYPTENDNDVHQKLFRKLVEDRAIFLSLCSNMFGNFFVQRVLECSNTEEQEILTEHLATDLYNLCLDKSACRVIQLAIQKLDVHLATRLSLELRDTHLVRLSIDQNGNHVIQKIVKTLPVSSWTFLVDFFADDDNLIHVCQDKYGCRVIQSTVETLSTDQYAQCYQHRVILLRSLMAGVTRNCTQLASNEFANYVVQHVIKCGDALAVYRDIIIEQCLLQNLLSMSQEKYASHVVEVAFECAPYRLVAEMMNEIFEGYIPHPDTNRDALDILLFHQYGNYVVQQMIQTCVLGQNARDQKQSEMYGMWLEKIHGRVMRNAHRLERFSSGKKIIEALQSMSLY

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 2 polymer

description	RNA II-3
formula_weight	3735.2 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

CUGUAUCUUAUA

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	nat
entity_count	5

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	20

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6. Citations (1)

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length_a	160.774 Å
length_b	160.774 Å
length_c	99.550 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	2.800 Å
resolution_low	33.940 Å
r_factor	0.2484
r_work	0.2473
r_free	0.2707

fit	/app/data/saxs_computation/pt/9ptj/9ptj.fit
pddf	/app/data/pr_computation/pt/9ptj/9ptj.pr.out
profile	/app/data/saxs_computation/pt/9ptj/9ptj.dat

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

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)