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9u49

crystal structure of Cdn1 in complex with cA4

Method: X-RAY DIFFRACTION D_max: 101.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u49
deposition_date	2025-03-19
last_revision	2026-02-04
title	crystal structure of Cdn1 in complex with cA4
keywords	Complex, CARF, RNA BINDING PROTEIN/RNA, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
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	31.11 Å
rg_electron	30.74 Å
i0	121841000.00
molecular_weight	91492.0 kDa
excluded_volume	116020 Å³
envelope_volume	144530 Å³
shell_volume	39714 Å³
envelope_diameter	104.1 Å
shell_rg	37.38 Å
envelope_rg	30.72 Å
shape_rg	30.72 Å
total_rg	31.42 Å
total_atoms	6471
n_residues	802
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	101.1 Å
rg_real	31.09 Å
rg_real_error	0.77 Å
i0_real	1.2180e+08
i0_real_error	1.8610e+06
rg_reciprocal	31.10 Å
i0_reciprocal	121800000.0000
total_estimate	0.8913
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.7 Å
skewness	0.316
kurtosis	-0.438
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	63660000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.900

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	CARF-domain containing dual-activated nuclease
formula_weight	46382.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7302

MKTLFVTATGQTEANYYTIWHLFRSQTNIEKIVVLSTDFTRKKNLLSNLMELLNLLDTGIHVEELHLPDGIEEKSISDIKAVIYQWIDNNQPKEIIFNVTGGTKLISFAQDQIAANNPNYSCVYQSWSNNQLVWYNTPDKPLEDIILPENIAVRLKGHGYDQISSETAFLDLPIEQYHYIAQLYKLIKIDFTKAQRLVSYLNYLVSSFDQKAVSYPYCFEIKKEGSFLSLAGWIKTLAQAAKPFIQLESLDDQKSKITFMSKEAAEFIGGKWFEVLVGFLITAYYQKKQTLVNIQIGLTFAKSSDGNEIDVAYLLKGHFYWMECKTVNWLKKNAPTTEVNNNLHKLSSISQGAGLNSHKFFVSLYDISEQSRKVAEDLGVIVIAGTDLFKFDRFLGEVAHHHHHH

Source

organism	Psychrobacter lutiphocae DSM 21542
ncbi_taxonomy_id	1123033
host_organism	Escherichia coli

Entity 2 polymer

description	cyclic tetra-adenosine monophosphate(cA4)
formula_weight	1271.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

AAAA

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	809

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6. Citations (1)

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length_a	89.930 Å
length_b	132.440 Å
length_c	75.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.900 Å
resolution_low	32.930 Å
r_factor	0.1900
r_work	0.1892
r_free	0.2267

fit	/app/data/saxs_computation/u4/9u49/9u49.fit
pddf	/app/data/pr_computation/u4/9u49/9u49.pr.out
profile	/app/data/saxs_computation/u4/9u49/9u49.dat

crystal structure of Cdn1 in complex with cA4

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)