Download MendeleyStructural evidence for a concerted Bifunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii
Bynck, J.H., Willemoes, M., Larsen, S., Johansson, E.To be published.
2HXD
Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium
- PDB DOI: https://doi.org/10.2210/pdb2HXD/pdb
- Classification: HYDROLASE
- Organism(s): Methanocaldococcus jannaschii
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2006-08-03 Released: 2007-08-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.221
- R-Value Work: 0.178
This is version 1.4 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 |
| dCTP deaminase, dUMP-forming | 204 | Methanocaldococcus jannaschii | Mutation(s): 1 Gene Names: dcd EC: 3.5.4.30 |  | |
UniProt | |||||
Find proteins for Q57872 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57872 Go to UniProtKB: Q57872 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q57872 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DUP Query on DUP | C [auth A] | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N |  | ||
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.221
- R-Value Work: 0.178
- Space Group: I 4 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 171.513 | α = 90 |
| b = 171.513 | β = 90 |
| c = 171.513 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| DNA | data collection |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2007-08-14 Deposition Author(s): Bynck, J.H., Johansson, E.
Revision History (Full details and data files)
- Version 1.0: 2007-08-14
Type: Initial release - Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.2: 2017-10-18
Changes: Refinement description - Version 1.3: 2021-11-10
Changes: Database references, Derived calculations - Version 1.4: 2023-10-25
Changes: Data collection, Refinement description
