Download MendeleyCrystal structure of dUTPase from Sulfolobus tokodaii
Kanagawa, M., Baba, S., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.To be published.
2ZDC
Crystal structure of dUTPase from Sulfolobus tokodaii
- PDB DOI: https://doi.org/10.2210/pdb2ZDC/pdb
- Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
- Organism(s): Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-11-21 Released: 2008-05-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.256
- R-Value Work: 0.218
- R-Value Observed: 0.218
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| 167aa long hypothetical dUTPase | 169 | N/A | Mutation(s): 0 EC: 3.6.1.23 |  | |
UniProt | |||||
Find proteins for F9VNI5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VNI5 Go to UniProtKB: F9VNI5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F9VNI5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | E [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| SO4 Query on SO4 | D [auth A], F [auth B], G [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.256
- R-Value Work: 0.218
- R-Value Observed: 0.218
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.434 | α = 108.56 |
| b = 53.408 | β = 108.57 |
| c = 53.419 | γ = 108.48 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2008-05-27 Deposition Author(s): Kanagawa, M., Baba S., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2008-05-27
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2024-11-20
Changes: Structure summary
