1ca5

INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA

Method: X-RAY DIFFRACTION Dmax: 47.1 Å Quality: GOOD

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

CHROMOSOMAL PROTEIN SAC7D

OrganismNot specified

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric(3) Consistent with all polymer counts Chain A; UniProt 1–65 Not recorded 5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3' × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;pH 6.5, VAPOR DIFFUSION, HANGING DROP Resolution 2.20 Å R-free 0.276

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 DN71_SULAC
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 2–66; UniProt 1–65

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 1ca5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ca5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ca5
Deposition date deposition_date1999-02-23
Structure title titleINTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA
Keywords keywordsHYPERTHERMOPHILE, CHROMOSOMAL PROTEIN, SSO7D, SAC7D, DNA BINDING, STRUCTURAL PROTEIN-DNA COMPLEX; STRUCTURAL PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier14.49
Radius of gyration Rg (electron density) rg_electron13.49
Forward intensity I(0) i04526940.00
Molecular weight molecular_weight12315.0 kDa
Excluded volume excluded_volume14182 ų
Envelope volume envelope_volume16704 ų
Hydration-shell volume shell_volume10800 ų
Envelope diameter envelope_diameter45.7
Shell Rg shell_rg18.85
Envelope Rg envelope_rg13.81
Shape Rg shape_rg13.41
Total Rg total_rg14.63
Total atoms total_atoms883
Residues n_residues81
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 dmax47.1
Rg (real space) rg_real14.42
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real4.5270e+06
I(0) uncertainty (real space) i0_real_error5.1340e+04
Rg (reciprocal space) rg_reciprocal14.42
I(0) (reciprocal space) i0_reciprocal4527000.0000
Solution quality estimate total_estimate0.8885
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.5
Skewness Skewness skewness0.171
Kurtosis Kurtosis kurtosis-0.347
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha438900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.984

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_idd1ca5a_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.1 — Histone-like proteins from archaea

CATH v4.4 (1 domains)

Domain ID domain_id1ca5A00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40

8. Citations (3)

9. Files and Curves (10)