Download MendeleyCrystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine
Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.To be published.
6MJK
Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine
- PDB DOI: https://doi.org/10.2210/pdb6MJK/pdb
- Classification: HYDROLASE
- Organism(s): Naegleria fowleri
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-09-21 Released: 2018-10-31
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.170
- R-Value Work: 0.134
- R-Value Observed: 0.137
wwPDB Validation 3D Report Full Report
Currently 6MJK does not have a validation slider image.
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| dUTP pyrophosphatase | 155 | Naegleria fowleri | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A0A1Z0YU86 (Naegleria fowleri) Explore A0A1Z0YU86 Go to UniProtKB: A0A1Z0YU86 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A1Z0YU86 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DUR Query on DUR | D [auth A] | 2'-DEOXYURIDINE C9 H12 N2 O5 MXHRCPNRJAMMIM-SHYZEUOFSA-N |  | ||
| PPV Query on PPV | E [auth A] | PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N |  | ||
| MG Query on MG | B [auth A], C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.170
- R-Value Work: 0.134
- R-Value Observed: 0.137
- Space Group: P 21 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.23 | α = 90 |
| b = 74.23 | β = 90 |
| c = 74.23 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Structure Validation
Currently 6MJK does not have a validation slider image.
Entry History
Deposition Data
- Released Date: 2018-10-31 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2018-10-31
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
