Download MendeleyCrystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E
Abendroth, J., Weiss, M.J., Calhoun, B., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.To be published.
7N56 | pdb_00007n56
Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E
- PDB DOI: https://doi.org/10.2210/pdb7N56/pdb
- Classification: HYDROLASE
- Organism(s): Rickettsia prowazekii str. Madrid E
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2021-06-04 Released: 2021-07-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.201 (Depositor), 0.200 (DCC)
- R-Value Work: 0.159 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.160 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| Deoxyuridine 5'-triphosphate nucleotidohydrolase | 152 | Rickettsia prowazekii str. Madrid E | Mutation(s): 0 Gene Names: dut, RP399 EC: 3.6.1.23 |  | |
UniProt | |||||
Find proteins for Q9ZDD2 (Rickettsia prowazekii (strain Madrid E)) Explore Q9ZDD2 Go to UniProtKB: Q9ZDD2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9ZDD2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | M [auth B], N [auth C], O [auth F] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.201 (Depositor), 0.200 (DCC)
- R-Value Work: 0.159 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.160 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 100.37 | α = 90 |
| b = 97.39 | β = 118.597 |
| c = 100.54 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MoRDa | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2021-07-07 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2021-07-07
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
