Download MendeleySignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins
Yu, Y., Jeffreys, L.N., Poddar, H., Hill, A., Johannissen, L., Dai, F., Sakuma, M., Leys, D., Heyes, D.J., Zhang, S., Scrutton, N.S.To be published.
8JBS
B12-binding domain from Chloracidobacterium thermophilum MerR family protein, dark state
- PDB DOI: https://doi.org/10.2210/pdb8JBS/pdb
- Classification: TRANSCRIPTION
- Organism(s): Chloracidobacterium thermophilum
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2023-05-09 Released: 2024-11-13
- Funding Organization(s): Engineering and Physical Sciences Research Council
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.236
- R-Value Work: 0.185
- R-Value Observed: 0.188
Starting Model: in silico
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative cobalamin binding protein | 327 | Chloracidobacterium thermophilum | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| B12 (Subject of Investigation/LOI) Query on B12 | C [auth A], E [auth B] | COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N |  | ||
| 5AD (Subject of Investigation/LOI) Query on 5AD | D [auth A], F [auth B] | 5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.236
- R-Value Work: 0.185
- R-Value Observed: 0.188
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 125.218 | α = 90 |
| b = 125.218 | β = 90 |
| c = 73.088 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DIALS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Engineering and Physical Sciences Research Council | United Kingdom | EP/S030336/1 |
Revision History (Full details and data files)
- Version 1.0: 2024-11-13
Type: Initial release
