2i4i

Crystal Structure of human DEAD-box RNA helicase DDX3X

Method: X-RAY DIFFRACTION Dmax: 91.9 Å Quality: GOOD

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

ATP-dependent RNA helicase DDX3X

Homo sapiens

UniProt O00571

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 167–581 Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;277 K;1.75M Na formate, 0.1M Tris pH 7.5, 20mM ATPgS and MgCl2, VAPOR DIFFUSION, temperature 277K Resolution 2.20 Å R-free 0.218

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.

16 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DDX3X_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–417; UniProt 167–581

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2i4i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2i4i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2i4i
Deposition date deposition_date2006-08-22
Structure title titleCrystal Structure of human DEAD-box RNA helicase DDX3X
Keywords keywordsRNA, HELICASE, DEAD, STRUCTURAL GENOMICS, SGC, Structural Genomics Consortium, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.25
Radius of gyration Rg (electron density) rg_electron25.39
Forward intensity I(0) i037751500.00
Molecular weight molecular_weight46526.0 kDa
Excluded volume excluded_volume57999 ų
Envelope volume envelope_volume73094 ų
Hydration-shell volume shell_volume24920 ų
Envelope diameter envelope_diameter94.3
Shell Rg shell_rg31.59
Envelope Rg envelope_rg25.44
Shape Rg shape_rg25.41
Total Rg total_rg26.05
Total atoms total_atoms3266
Residues n_residues408
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax91.9
Rg (real space) rg_real26.33
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real3.7750e+07
I(0) uncertainty (real space) i0_real_error5.2420e+05
Rg (reciprocal space) rg_reciprocal26.31
I(0) (reciprocal space) i0_reciprocal37750000.0000
Solution quality estimate total_estimate0.8549
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0
Skewness Skewness skewness0.408
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha10690000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2i4ia1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches
Domain ID domain_idd2i4ia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2i4ia3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2i4iA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2i4iA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)