1yqr

Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA

Method: X-RAY DIFFRACTION Dmax: 74.3 Å Quality: GOOD

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

N-glycosylase/DNA lyase

Homo sapiens

UniProt O15527

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 12–327 Fragment:8-OXOGUANINE DNA GLYCOSYLASE Mutation:N149C,K249Q 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' × 1 5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.43 Å R-free 0.251

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.

46 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OGG1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 4–319; UniProt 12–327

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 1yqr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1yqr
Deposition date deposition_date2005-02-02
Structure title titleCatalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA
Keywords keywordsDisulfide crosslinking, crosslinking validation, 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_guinier22.45
Radius of gyration Rg (electron density) rg_electron21.17
Forward intensity I(0) i041312700.00
Molecular weight molecular_weight43665.0 kDa
Excluded volume excluded_volume51926 ų
Envelope volume envelope_volume62640 ų
Hydration-shell volume shell_volume24427 ų
Envelope diameter envelope_diameter75.0
Shell Rg shell_rg28.44
Envelope Rg envelope_rg21.42
Shape Rg shape_rg21.14
Total Rg total_rg22.03
Total atoms total_atoms3040
Residues n_residues341
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 dmax74.3
Rg (real space) rg_real22.35
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real4.1310e+07
I(0) uncertainty (real space) i0_real_error5.1420e+05
Rg (reciprocal space) rg_reciprocal22.38
I(0) (reciprocal space) i0_reciprocal41310000.0000
Solution quality estimate total_estimate0.8797
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5605000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.941

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1yqra1
Class classa — All alpha proteins
Fold Fold folda.96 — DNA-glycosylase
Superfamily Superfamily superfamilya.96.1 — DNA-glycosylase
Family Family familya.96.1.3 — DNA repair glycosylase, 2 C-terminal domains
Domain ID domain_idd1yqra2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.2 — DNA repair glycosylase, N-terminal domain
Domain ID domain_idd1yqra3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id1yqrA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily40
Domain ID domain_id1yqrA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id1yqrA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2

8. Citations (1)

9. Files and Curves (10)