1kqq

Solution Structure of the Dead ringer ARID-DNA Complex

Method: SOLUTION NMR Dmax: 55.1 Å Quality: EXCELLENT

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

DEAD RINGER PROTEIN

Drosophila melanogaster

UniProt Q24573

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric(3) Consistent with all polymer counts Chain A; UniProt 262–398 Fragment:A/T Rich Interaction Domain Mutation:F355L 5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3' × 1 5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3' × 1 SOLUTION NMR NMR measurement conditions:pH 6.7;310 K;Ionic strength (raw mmCIF value) 0;Pressure ambient NMR sample composition:2.0mM Dead ringer-DNA complex (protein U-13C,15N, DNA NA) 20mM Tris U-2H, 0.01% NaN3 NA, 0.5mM EDTA NA, 5mM DTT U-2H | 93% H2O/7% D2O NMR sample composition:1.4mM Dead ringer-DNA complex (protein U-13C,15N, DNA NA) 20mM Tris U-2H, 0.01% NaN3 NA, 0.5mM EDTA NA, 5mM DTT U-2H | 100% D2O Resolution not provided

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.

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

View Construct and Data Evidence
UniProt name DRI_DROME
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 3–139; UniProt 262–398

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 1kqq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1kqq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1kqq
Deposition date deposition_date2002-01-07
Structure title titleSolution Structure of the Dead ringer ARID-DNA Complex
Keywords keywordsARID, PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier19.18
Radius of gyration Rg (electron density) rg_electron18.47
Forward intensity I(0) i04942470000.00
Molecular weight molecular_weight488560.0 kDa
Excluded volume excluded_volume565270 ų
Envelope volume envelope_volume45979 ų
Hydration-shell volume shell_volume19829 ų
Envelope diameter envelope_diameter64.5
Shell Rg shell_rg25.90
Envelope Rg envelope_rg19.73
Shape Rg shape_rg18.43
Total Rg total_rg18.64
Total atoms total_atoms62400
Residues n_residues3220
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 dmax55.1
Rg (real space) rg_real19.11
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real4.9420e+09
I(0) uncertainty (real space) i0_real_error5.9270e+07
Rg (reciprocal space) rg_reciprocal19.12
I(0) (reciprocal space) i0_reciprocal4942000000.0000
Solution quality estimate total_estimate0.9164
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.8
Skewness Skewness skewness0.152
Kurtosis Kurtosis kurtosis-0.599
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1402000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.959

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1kqqa_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.3 — ARID-like
Family Family familya.4.3.1 — ARID domain

CATH v4.4 (1 domains)

Domain ID domain_id1kqqA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily60 — ARID DNA-binding domain

8. Citations (1)

9. Files and Curves (10)