1xnt

NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN

Method: SOLUTION NMR Dmax: 46.9 Å Quality: REASONABLE

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

PROTEIN (DNA-REPAIR PROTEIN XRCC1)

Homo sapiens

UniProt P18887

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 1–183 Fragment:N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN. Mutation:D179E No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6.8;298 K;Ionic strength (raw mmCIF value) 0.4;Pressure 1 NMR sample composition:H2O AND 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.

10 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XRCC1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–183; UniProt 1–183

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 1xnt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xnt
Deposition date deposition_date1999-02-27
Structure title titleNMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN
Keywords keywordsXRCC1, 3D NMR, DNA REPAIR, SINGLE-STRAND BREAK DNA BINDING, DNA POLYMERASE- BETA BINDING, BETA SANDWICH, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier15.27
Radius of gyration Rg (electron density) rg_electron14.76
Forward intensity I(0) i02189070000.00
Molecular weight molecular_weight383200.0 kDa
Excluded volume excluded_volume473770 ų
Envelope volume envelope_volume32331 ų
Hydration-shell volume shell_volume16400 ų
Envelope diameter envelope_diameter54.8
Shell Rg shell_rg22.67
Envelope Rg envelope_rg16.74
Shape Rg shape_rg14.73
Total Rg total_rg14.96
Total atoms total_atoms53429
Residues n_residues3473
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 dmax46.9
Rg (real space) rg_real15.19
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real2.1890e+09
I(0) uncertainty (real space) i0_real_error2.5720e+07
Rg (reciprocal space) rg_reciprocal15.19
I(0) (reciprocal space) i0_reciprocal2189000000.0000
Solution quality estimate total_estimate0.6839
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.2
Skewness Skewness skewness0.164
Kurtosis Kurtosis kurtosis-0.408
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha501100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 0.999; Sysdev: 0.368; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1xnta_
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.8 — N-terminal domain of xrcc1

CATH v4.4 (1 domains)

Domain ID domain_id1xntA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like

8. Citations (1)

9. Files and Curves (10)