SAXSdb — 9uu7

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable ATP-dependent RNA helicase DDX28

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 126–357 Chain B； UniProt 126–357	Not recorded	PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；25% PEG 3350, 0.2 M Lithium sulphat, 0.1M Tris, pH 8.5	Resolution 2.60 Å R-free 0.277

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9UU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7OI6 Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1 Deposited 2021-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric	Chain x 1–540（540 aa）	Not recorded	MG MAGNESIUM ION × 48 ZN ZINC ION × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DDX28_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 126–357 Author chain B； PDBConstruct 1–232； UniProt 126–357

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9uu7
Deposition date deposition_date	2025-05-06
Structure title title	The crystal structure of human DEAD-box RNA helicase DDX28 RecA1 domain in complex with ADP
Keywords keywords	DEAD-box RNA helicase, mitoribosome assembly, RIBOSOMAL PROTEIN; RIBOSOMAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.26 Å
Radius of gyration Rg (electron density) rg_electron	24.38 Å
Forward intensity I(0) i0	36859700.00
Molecular weight molecular_weight	47800.0 kDa
Excluded volume excluded_volume	60394 Å³
Envelope volume envelope_volume	72554 Å³
Hydration-shell volume shell_volume	25404 Å³
Envelope diameter envelope_diameter	84.4 Å
Shell Rg shell_rg	31.03 Å
Envelope Rg envelope_rg	24.63 Å
Shape Rg shape_rg	24.40 Å
Total Rg total_rg	25.15 Å
Total atoms total_atoms	3368
Residues n_residues	462
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	80.8 Å
Rg (real space) rg_real	25.32 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.6860e+07
I(0) uncertainty (real space) i0_real_error	4.8730e+05
Rg (reciprocal space) rg_reciprocal	25.30 Å
I(0) (reciprocal space) i0_reciprocal	36860000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.439
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9830000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Probable ATP-dependent RNA helicase DDX28
Molecular weight formula_weight	24830.6 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	3379

GSFADLGLEPRVLHALQEAAPEVVQPTTVQSSTIPSLLRGRHVVCAAETGSGKTLSYLLPLLQRLLGQPSLDSLPIPAPRGLVLVPSRELAQQVRAVAQPLGRSLGLLVRDLEGGHGMRRIRLQLSRQPSADVLVATPGALWKALKSRLISLEQLSFLVLDEADTLLDESFLELVDYILEKSHIAEGPADLEDPFNPKAQLVLVGATFPEGVGQLLNKVASPDAVTTITSSK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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8. Citations (1)

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Unit-cell length a length_a	43.260 Å
Unit-cell length b length_b	67.201 Å
Unit-cell length c length_c	147.501 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.730 Å
R factor r_factor	0.2313
R_work r_work	0.2289
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable ATP-dependent RNA helicase DDX28

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction