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9uu7

The crystal structure of human DEAD-box RNA helicase DDX28 RecA1 domain in complex with ADP

Method: X-RAY DIFFRACTION D_max: 80.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uu7
deposition_date	2025-05-06
title	The crystal structure of human DEAD-box RNA helicase DDX28 RecA1 domain in complex with ADP
keywords	DEAD-box RNA helicase, mitoribosome assembly, RIBOSOMAL PROTEIN; RIBOSOMAL 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	25.26 Å
rg_electron	24.38 Å
i0	36859700.00
molecular_weight	47800.0 kDa
excluded_volume	60394 Å³
envelope_volume	72554 Å³
shell_volume	25404 Å³
envelope_diameter	84.4 Å
shell_rg	31.03 Å
envelope_rg	24.63 Å
shape_rg	24.40 Å
total_rg	25.15 Å
total_atoms	3368
n_residues	462
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	80.8 Å
rg_real	25.32 Å
rg_real_error	0.49 Å
i0_real	3.6860e+07
i0_real_error	4.8730e+05
rg_reciprocal	25.30 Å
i0_reciprocal	36860000.0000
total_estimate	0.8858
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.9 Å
skewness	0.439
kurtosis	-0.356
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	9830000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.956

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Probable ATP-dependent RNA helicase DDX28
formula_weight	24830.6 kDa
ec_number	3.6.4.13
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	3379

GSFADLGLEPRVLHALQEAAPEVVQPTTVQSSTIPSLLRGRHVVCAAETGSGKTLSYLLPLLQRLLGQPSLDSLPIPAPRGLVLVPSRELAQQVRAVAQPLGRSLGLLVRDLEGGHGMRRIRLQLSRQPSADVLVATPGALWKALKSRLISLEQLSFLVLDEADTLLDESFLELVDYILEKSHIAEGPADLEDPFNPKAQLVLVGATFPEGVGQLLNKVASPDAVTTITSSK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	11

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6. Citations (1)

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length_a	43.260 Å
length_b	67.201 Å
length_c	147.501 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.600 Å
resolution_low	19.730 Å
r_factor	0.2313
r_work	0.2289
r_free	0.2771

fit	/app/data/saxs_computation/uu/9uu7/9uu7.fit
pddf	/app/data/pr_computation/uu/9uu7/9uu7.pr.out
profile	/app/data/saxs_computation/uu/9uu7/9uu7.dat

The crystal structure of human DEAD-box RNA helicase DDX28 RecA1 domain in complex with ADP

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