Ribose import binding protein RbsB
UniProt P02925 · gene rbsB · Escherichia coli (strain K12) · 296 residues
18evidence items
6mapped to a state
2states
4techniques
4sources
0conflicts
Coverage grid
Mapped evidence per state and technique. Shaded rows rest on a single technique. Badge = best data level in the cell: raw (traces, images, FIDs: can be re-analysed), proc (maps, curves, tables, trajectories) or rep (values in the paper only).
| State | Basis | xray | saxs_sans | af_prediction | md | Total |
|---|---|---|---|---|---|---|
| open, ligand-free RBP-open | observed (one method) | proc 1 | · | · | · | 1 |
| closed, ribose-bound RBP-closed | observed (one method) | proc 5 | · | · | · | 5 |
Unmapped evidence: 12 of 18 items. Mappings come from curator assignments and curated rules; see About for how rules work.
Sources
| Source | Evidence | Mapped |
|---|---|---|
| AlphaFold DB | 1 | 0 |
| MDDB | 1 | 0 |
| RCSB PDB | 7 | 6 |
| SASBDB | 9 | 0 |
Curated rules applied
rbp-ribose-closed: 4 items
Structure
Choose a state. Each model is badged observed or inferred; assumptions are one click away.
States and transitions
| State | Basis | Parent | Description |
|---|---|---|---|
| open, ligand-free RBP-open | observed | — | Ligand-free open form, as in 1URP. |
| closed, ribose-bound RBP-closed | observed | — | Closed form with D-ribose bound, as in 2DRI. |
No transitions recorded in this version (no rate or free-energy evidence has been curated yet).
Evidence
One row per deposit or experiment. Filter by technique, environment or text. Unmapped evidence is listed too.
| Evidence | Technique | Observable | Conditions | Mapped to state |
|---|---|---|---|---|
| EV-PDB-1BA2-1 RCSB PDB | xray | resolution: 2.1 Å | in vitro · -183.15 °C · pH 7 D67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI · D-RIBOSE-BINDING PROTEIN (chains A,B) | unmapped |
| EV-PDB-1DBP-1 RCSB PDB | xray | resolution: 2.2 Å | in vitro · ligands RIP IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS · D-RIBOSE-BINDING PROTEIN (chains A) | closed, ribose-bound · rule:rbp-ribose-closed · high Ribose (RIP) bound closes the two domains. |
| EV-PDB-1DRJ-1 RCSB PDB | xray | resolution: 2.5 Å | in vitro · ligands RIP PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS · D-RIBOSE-BINDING PROTEIN (chains A) | closed, ribose-bound · rule:rbp-ribose-closed · high Ribose (RIP) bound closes the two domains. |
| EV-PDB-1DRK-1 RCSB PDB | xray | resolution: 2 Å | in vitro · ligands RIP PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS · D-RIBOSE-BINDING PROTEIN (chains A) | closed, ribose-bound · rule:rbp-ribose-closed · high Ribose (RIP) bound closes the two domains. |
| EV-PDB-1URP-1 RCSB PDB | xray | resolution: 2.3 Å | in vitro · -183.15 °C · pH 5 D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI · D-RIBOSE-BINDING PROTEIN (chains A,B,C,D) | open, ligand-free · curator:draft (unreviewed) · high Ligand-free D-ribose-binding protein. |
| EV-PDB-2DRI-1 RCSB PDB | xray | resolution: 1.6 Å | in vitro · ligands RIP PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS · D-RIBOSE-BINDING PROTEIN (chains A) | closed, ribose-bound · curator:draft (unreviewed) · high Ribose (RIP) bound. |
| EV-PDB-2GX6-1 RCSB PDB | xray | resolution: 1.97 Å | in vitro · -173.15 °C · pH 5 · ligands RIP Rational stabilization of E. coli ribose binding protein · D-ribose-binding periplasmic protein (chains A) | closed, ribose-bound · rule:rbp-ribose-closed · high Ribose (RIP) bound closes the two domains. |
| EV-SASBDB-SASDSB9 SASBDB | saxs_sans | radius_of_gyration: 2.086 nm ± 0.002 | in vitro · 4 °C · pH 7 SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB | unmapped |
| EV-SASBDB-SASDSC9 SASBDB | saxs_sans | radius_of_gyration: 2.1 nm ± 0.003 | in vitro · 4 °C · pH 7 SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB | unmapped |
| EV-SASBDB-SASDSD9 SASBDB | saxs_sans | radius_of_gyration: 2.123 nm ± 0.003 | in vitro · 4 °C · pH 7 SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB | unmapped |
| EV-SASBDB-SASDSE9 SASBDB | saxs_sans | radius_of_gyration: 2.04 nm ± 0.002 | in vitro · 4 °C · pH 7 · ligands partner: Ribose SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB with Ribose | unmapped |
| EV-SASBDB-SASDSF9 SASBDB | saxs_sans | radius_of_gyration: 2.046 nm ± 0.003 | in vitro · 4 °C · pH 7 · ligands partner: Ribose SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB with Ribose | unmapped |
| EV-SASBDB-SASDSG9 SASBDB | saxs_sans | radius_of_gyration: 2.078 nm ± 0.004 | in vitro · 4 °C · pH 7 · ligands partner: Ribose SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB with Ribose | unmapped |
| EV-SASBDB-SASDTB2 SASBDB | saxs_sans | radius_of_gyration: 2.465 nm ± 0.201 | in vitro · 22 °C · pH 7 SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB | unmapped |
| EV-SASBDB-SASDTC2 SASBDB | saxs_sans | radius_of_gyration: 2.241 nm ± 0.185 | in vitro · 22 °C · pH 7 · ligands partner: Ribose SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB with Ribose | unmapped |
| EV-SASBDB-SASDTD2 SASBDB | saxs_sans | radius_of_gyration: 1.919 nm ± 0.182 | in vitro · 22 °C · pH 7 · ligands partner: Ribose SAXS/WAXS data of conformationally flexible ribose binding protein · Ribose import binding protein RbsB with Ribose | unmapped |
| EV-AFDB-AF-P02925-F1 AlphaFold DB | af_prediction | plddt: 94.5 pLDDT | in silico AlphaFold DB prediction AF-P02925-F1 · AlphaFold Monomer v2.0 pipeline, residues 1-296 | unmapped |
| EV-MDDB-A00BA MDDB | md | trajectory: 10 ns | in silico · 26.85 °C MoDEL 2DRI · start 2DRI; Amber Parm99 | unmapped |
Conflicts
No conflicts found among comparable evidence.
9 evidence items could not be compared: they lack a comparable observable type, a value, or an uncertainty. Absence of a conflict here is not agreement.
Downloads
- Protein bundle (JSON)
- RBP-open-cif (mmCIF, observed)
- RBP-open-pdb (PDB, observed)
- RBP-closed-cif (mmCIF, observed)
- RBP-closed-pdb (PDB, observed)
- Curation file (YAML)