Download MendeleyThe crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1
Chen, Y.Q., Zhang, J., Gan, J.H.To be published.
5HRG | pdb_00005hrg
The crystal structure of AsfvPolX(D51N mutant):DNA4 binary complex
- PDB DOI: https://doi.org/10.2210/pdb5HRG/pdb
- NAKB: 5HRG
- Classification: TRANSFERASE/DNA
- Organism(s): African swine fever virus, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2016-01-23 Released: 2017-01-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 ?
- R-Value Free: 0.239 (Depositor), 0.250 (DCC)
- R-Value Work: 0.191 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.193 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| DNA polymerase beta-like protein | 178 | African swine fever virus | Mutation(s): 1 Gene Names: O174L EC: 2.7.7.7 |  | |
UniProt | |||||
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore P42494 Go to UniProtKB: P42494 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P42494 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3') | 8 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | F [auth A], G [auth A], I [auth B], J [auth B], K [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| MN Query on MN | E [auth A], H [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 ?
- R-Value Free: 0.239 (Depositor), 0.250 (DCC)
- R-Value Work: 0.191 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.193 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 44.06 | ¦Á = 68.35 |
| b = 51.17 | ¦Â = 86.25 |
| c = 55.54 | ¦Ă = 88.2 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-01-18 Deposition Author(s): Chen, Y.Q., Zhang, J., Gan, J.H.
Revision History (Full details and data files)
- Version 1.0: 2017-01-18
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-11-06
Changes: Structure summary
