9zd6

Bacterial interstrand DNA crosslink glycosylase AlkX/YcaQ bound to DNA

Method: X-RAY DIFFRACTION Dmax: 95.0 Å Quality: EXCELLENT

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

Cytoplasmic protein

Thermobifida fusca

UniProt Q47TC5

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 1–402 Chain B; UniProt 1–402 Non-standard monomer:Yes (specific site not provided by mmCIF) ;DNA (5'-D(*TP*GP*AP*GP*TP*CP*GP*T*(3DR)P*GP*AP*TP*GP*AP*CP*CP*AP*C)-3') ; × 1 ;DNA (5'-D(*GP*TP*GP*GP*TP*CP*AP*TP*CP*CP*AP*CP*GP*AP*CP*TP*CP*A)-3') ; × 1 EDO 1,2-ETHANEDIOL × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;294 K;100 mM MES/imidazole pH 6.5, 30 mM NaF, 30 mM NaCl, 30 mM NaI, 10% PEG4000, 10% glycerol Resolution 2.60 Å R-free 0.256

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q47TC5_THEFY
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–402; UniProt 1–402 Author chain B; PDBConstruct 1–402; UniProt 1–402

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 9zd6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zd6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zd6
Deposition date deposition_date2025-11-24
最后修订 last_revision2026-01-14
Structure title titleBacterial interstrand DNA crosslink glycosylase AlkX/YcaQ bound to DNA
Keywords keywordsDNA glycosylase, interstrand DNA crosslink, hydrolase, HYDROLASE-DNA complex; HYDROLASE/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.92
Radius of gyration Rg (electron density) rg_electron30.54
Forward intensity I(0) i0180968000.00
Molecular weight molecular_weight97665.0 kDa
Excluded volume excluded_volume118330 ų
Envelope volume envelope_volume156320 ų
Hydration-shell volume shell_volume42206 ų
Envelope diameter envelope_diameter98.7
Shell Rg shell_rg38.39
Envelope Rg envelope_rg29.75
Shape Rg shape_rg30.56
Total Rg total_rg31.16
Total atoms total_atoms6837
Residues n_residues794
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 dmax95.0
Rg (real space) rg_real30.77
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real1.8100e+08
I(0) uncertainty (real space) i0_real_error2.9970e+06
Rg (reciprocal space) rg_reciprocal30.83
I(0) (reciprocal space) i0_reciprocal181000000.0000
Solution quality estimate total_estimate0.9087
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.2
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26980000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.966

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)