Download MendeleyCrystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica
Stogios, P.J.To be published.
6B5F
Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica
- PDB DOI: https://doi.org/10.2210/pdb6B5F/pdb
- Classification: TRANSFERASE
- Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-09-29 Released: 2017-10-18
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.180
- R-Value Work: 0.150
- R-Value Observed: 0.151
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 354 | Yersinia enterocolitica subsp. enterocolitica 8081 | Mutation(s): 0 Gene Names: cobT, YE2707 EC: 2.4.2.21 |  | |
UniProt | |||||
Find proteins for A1JTP8 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JTP8 Go to UniProtKB: A1JTP8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1JTP8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], E [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.180
- R-Value Work: 0.150
- R-Value Observed: 0.151
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.155 | α = 90 |
| b = 73.875 | β = 90 |
| c = 119 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHENIX | phasing |
| PHENIX | model building |
| Coot | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-10-18 Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Grimshaw, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201200026C |
Revision History (Full details and data files)
- Version 1.0: 2017-10-18
Type: Initial release - Version 1.1: 2019-12-11
Changes: Author supporting evidence - Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
