2dkf
Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily
1. Protein Identity and Related Structures Protein Identity & Related Structures
No usable UniProt protein identity is available for this entry.
The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.
Assembly Composition of the Current Entry
| Assembly | Physical composition | Protein state | 蛋白 / DNA / RNA / 其他Polymer | Data consistency |
|---|---|---|---|---|
| 1 | Protein monomer | Monomer | 1 / 0 / 0 / 0 | Consistent with protein count |
| 2 | Protein monomer | Monomer | 1 / 0 / 0 / 0 | Consistent with protein count |
| 3 | Protein monomer | Monomer | 1 / 0 / 0 / 0 | Consistent with protein count |
| 4 | Protein monomer | Monomer | 1 / 0 / 0 / 0 | Consistent with protein count |
| 5 | Protein homooligomer | Homooligomer | 2 / 0 / 0 / 0 | Consistent with protein count |
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.
2. Structure Basics 2. Structure Basics
| Entry ID entry_id | 2dkf |
| Deposition date deposition_date | 2006-04-10 |
| Structure title title | Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily |
| Keywords keywords | ;beta-CASP family, metallo-beta-lactamase, ribonuclease, RNase E, Thermus thermophilus, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, hydrolase ;; HYDROLASE |
| Experimental Method method | X-RAY DIFFRACTION |
3. Official assembly/model SAXS Official SAXS Profiles
This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.
2dkf__assembly_2__model_1
Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)
2dkf__assembly_2__model_1 | I(q)
2dkf__assembly_2__model_1 | P(r) · Pending
| Rg（Guinier） | 22.72 Å |
| Rg (electron density) | 21.71 Å |
| Total Rg | 22.51 Å |
| Atom count | 3328 |
| Residues | 424 |
| Excluded volume | 59503 ų |
| Maximum q | 0.500 Å⁻¹ |
| Assembly | Model | Structure unit | Oligomeric description | Status | CRYSOL | Actions |
|---|---|---|---|---|---|---|
| 1 | 1 | 2dkf__assembly_1__model_1 |
monomeric （1） | Success | 4.1.3-1-20251215 (887e7ef) | View Download |
| 2 | 1 | 2dkf__assembly_2__model_1 |
monomeric （1） | Success | 4.1.3-1-20251215 (887e7ef) | View Download |
| 3 | 1 | 2dkf__assembly_3__model_1 |
monomeric （1） | Success | 4.1.3-1-20251215 (887e7ef) | View Download |
| 4 | 1 | 2dkf__assembly_4__model_1 |
monomeric （1） | Success | 4.1.3-1-20251215 (887e7ef) | View Download |
| 5 | 1 | 2dkf__assembly_5__model_1 |
dimeric （2） | Success | 4.1.3-1-20251215 (887e7ef) | View Download |
4. Crystallography and Experiment 4. Crystallography & Experiment
5. Entities and Polymers Entities & Polymers (3)
6. Fold Classification (SCOP + CATH) 12 domains
SCOP 2.08 (4 domains)
| Domain ID domain_id | d2dkfa1 |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.157 — Metallo-hydrolase/oxidoreductase |
| Superfamily Superfamily superfamily | d.157.1 — Metallo-hydrolase/oxidoreductase |
| Family Family family | d.157.1.10 — beta-CASP RNA-metabolising hydrolases |
| Domain ID domain_id | d2dkfb_ |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.157 — Metallo-hydrolase/oxidoreductase |
| Superfamily Superfamily superfamily | d.157.1 — Metallo-hydrolase/oxidoreductase |
| Family Family family | d.157.1.10 — beta-CASP RNA-metabolising hydrolases |
| Domain ID domain_id | d2dkfc_ |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.157 — Metallo-hydrolase/oxidoreductase |
| Superfamily Superfamily superfamily | d.157.1 — Metallo-hydrolase/oxidoreductase |
| Family Family family | d.157.1.10 — beta-CASP RNA-metabolising hydrolases |
| Domain ID domain_id | d2dkfd_ |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.157 — Metallo-hydrolase/oxidoreductase |
| Superfamily Superfamily superfamily | d.157.1 — Metallo-hydrolase/oxidoreductase |
| Family Family family | d.157.1.10 — beta-CASP RNA-metabolising hydrolases |
CATH v4.4 (8 domains)
| Domain ID domain_id | 2dkfA01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 60 — 4-Layer Sandwich |
| Topology topology | 15 — Metallo-beta-lactamase; Chain A |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like |
| Domain ID domain_id | 2dkfA02 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| Topology topology | 50 — Rossmann fold |
| Homologous superfamily homologous superfamily | 10890 — |
| Domain ID domain_id | 2dkfB01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 60 — 4-Layer Sandwich |
| Topology topology | 15 — Metallo-beta-lactamase; Chain A |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like |
| Domain ID domain_id | 2dkfB02 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| Topology topology | 50 — Rossmann fold |
| Homologous superfamily homologous superfamily | 10890 — |
| Domain ID domain_id | 2dkfC01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 60 — 4-Layer Sandwich |
| Topology topology | 15 — Metallo-beta-lactamase; Chain A |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like |
| Domain ID domain_id | 2dkfC02 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| Topology topology | 50 — Rossmann fold |
| Homologous superfamily homologous superfamily | 10890 — |
| Domain ID domain_id | 2dkfD01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 60 — 4-Layer Sandwich |
| Topology topology | 15 — Metallo-beta-lactamase; Chain A |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like |
| Domain ID domain_id | 2dkfD02 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| Topology topology | 50 — Rossmann fold |
| Homologous superfamily homologous superfamily | 10890 — |