8cmn

18mer DNA mimic Foldamer with an aliphatic linker in complex with Sac7d wild protein

Method: X-RAY DIFFRACTION Dmax: 51.2 Å Quality: GOOD

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

DNA-binding protein 7d

Sulfolobus acidocaldarius DSM 639

UniProt P13123

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 heterocomplex Heteromer Protein × 3 PDB declaration: monomeric(1) Count mismatch; review required Chain AA; UniProt 1–66 Not recorded N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293.15 K;10% PEG 400, 0.1 M MES pH 6.0 Resolution 2.65 Å R-free 0.297

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.

23 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DN7D_SULAC
Isoform
PDB entities 1
Chains and sequence ranges Author chain AA; PDBConstruct 1–66; UniProt 1–66

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 8cmn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8cmn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8cmn
Deposition date deposition_date2023-02-20
Structure title title18mer DNA mimic Foldamer with an aliphatic linker in complex with Sac7d wild protein
Keywords keywordsFoldamer, DNA mimic, DNA binding protein, histone; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.43
Radius of gyration Rg (electron density) rg_electron14.35
Forward intensity I(0) i03815960.00
Molecular weight molecular_weight12153.0 kDa
Excluded volume excluded_volume14310 ų
Envelope volume envelope_volume16570 ų
Hydration-shell volume shell_volume10492 ų
Envelope diameter envelope_diameter50.6
Shell Rg shell_rg19.01
Envelope Rg envelope_rg14.65
Shape Rg shape_rg14.26
Total Rg total_rg15.41
Total atoms total_atoms841
Residues n_residues63
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 dmax51.2
Rg (real space) rg_real15.44
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real3.8160e+06
I(0) uncertainty (real space) i0_real_error4.1210e+04
Rg (reciprocal space) rg_reciprocal15.44
I(0) (reciprocal space) i0_reciprocal3816000.0000
Solution quality estimate total_estimate0.8788
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.6
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.263
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha591600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.967

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)