Escherichia coli
| Assembly | Physical composition | Protein state | Molecular copy count | Associated components | Data consistency |
|---|---|---|---|---|---|
| 1 | Protein monomer | Monomer | Protein 1 | SULFATE ION × 7 ZINC ION × 5 water × 1 | Consistent with protein count |
| UniProt name | RND_ECOLI |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–375； UniProt 1–375 |
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.
| Entry ID entry_id | 1yt3 |
| Deposition date deposition_date | 2005-02-09 |
| Structure title title | Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing |
| Keywords keywords | RNase; exoribonuclease; ribonuclease; exonuclease; nuclease; hydrolase; tRNA processing, HYDROLASE, TRANSLATION; HYDROLASE,TRANSLATION |
| Experimental Method method | X-RAY DIFFRACTION |
This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.
Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)
| Rg（Guinier） | 25.04 Å |
| Rg (electron density) | 24.15 Å |
| Total Rg | 24.98 Å |
| Atom count | 3047 |
| Residues | 375 |
| Excluded volume | 54344 ų |
| Maximum q | 0.500 Å⁻¹ |
| Domain ID domain_id | d1yt3a1 |
| Class class | a — All alpha proteins |
| Fold Fold fold | a.60 — SAM domain-like |
| Superfamily Superfamily superfamily | a.60.8 — HRDC-like |
| Family Family family | a.60.8.3 — RNase D C-terminal domains |
| Domain ID domain_id | d1yt3a2 |
| Class class | a — All alpha proteins |
| Fold Fold fold | a.60 — SAM domain-like |
| Superfamily Superfamily superfamily | a.60.8 — HRDC-like |
| Family Family family | a.60.8.3 — RNase D C-terminal domains |
| Domain ID domain_id | d1yt3a3 |
| Class class | c — Alpha and beta proteins (a/b) |
| Fold Fold fold | c.55 — Ribonuclease H-like motif |
| Superfamily Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| Family Family family | c.55.3.5 — DnaQ-like 3'-5' exonuclease |
| Domain ID domain_id | 1yt3A01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| Domain ID domain_id | 1yt3A02 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 10 — Orthogonal Bundle |
| Topology topology | 150 — DNA polymerase; domain 1 |
| Homologous superfamily homologous superfamily | 80 — HRDC domain |
| Domain ID domain_id | 1yt3A03 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 10 — Orthogonal Bundle |
| Topology topology | 150 — DNA polymerase; domain 1 |
| Homologous superfamily homologous superfamily | 80 — HRDC domain |