Download MendeleyCrystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE (twinned lattice)
Liu, L., Lovell, S., Seibold, S., Battaile, K.P.To be published.
9YFK | pdb_00009yfk
Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE (twinned lattice)
- PDB DOI: https://doi.org/10.2210/pdb9YFK/pdb
- Classification: TRANSFERASE
- Organism(s): Bordetella pertussis Tohama I
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2025-09-26 Released: 2025-10-08
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.68 Å
- R-Value Free: 0.204 (Depositor), 0.207 (DCC)
- R-Value Work: 0.168 (Depositor), 0.175 (DCC)
- R-Value Observed: 0.178 (Depositor)
Starting Model: experimental
View more details
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 |
| UTP--glucose-1-phosphate uridylyltransferase | 285 | Bordetella pertussis Tohama I | Mutation(s): 0 Gene Names: BP3403 EC: 2.7.7.9 |  | |
UniProt | |||||
Find proteins for Q7VTV0 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTV0 Go to UniProtKB: Q7VTV0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7VTV0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UPG (Subject of Investigation/LOI) Query on UPG | C [auth A], E [auth B] | URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N |  | ||
| MG (Subject of Investigation/LOI) Query on MG | D [auth A], F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.68 Å
- R-Value Free: 0.204 (Depositor), 0.207 (DCC)
- R-Value Work: 0.168 (Depositor), 0.175 (DCC)
- R-Value Observed: 0.178 (Depositor)
Space Group: I 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93.397 | α = 90 |
| b = 71.027 | β = 90.06 |
| c = 93.487 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-10-08 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 75N93022C00036 |
| National Institutes of Health/Office of the Director | United States | S10OD030394 |
Revision History (Full details and data files)
- Version 1.0: 2025-10-08
Type: Initial release
