Download MendeleyPorcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
Tompkins, K.To be published.
6WDZ
Porcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
- DOI: 10.2210/pdb6WDZ/pdb
- NDB: 6WDZ
- Classification: REPLICATION/DNA
- Organism(s): Porcine circovirus 2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-04-01 Released: 2020-12-16
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.03 Å
- R-Value Free: 0.280
- R-Value Work: 0.229
- R-Value Observed: 0.232
wwPDB Validation 3D Report Full Report
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ATP-dependent helicase Rep | A, D, G | 115 | Porcine circovirus 2 | Mutation(s): 0 Gene Names: Rep |  |
Find proteins for A0A060L113 (Porcine circovirus 2) Explore A0A060L113 Go to UniProtKB: A0A060L113 | |||||
Protein Feature ViewExpand | |||||
| |||||
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3') | C, F, I, J | 10 | Porcine circovirus 2 |  | |
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | G | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| MN Query on MN | A, D, G | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.03 Å
- R-Value Free: 0.280
- R-Value Work: 0.229
- R-Value Observed: 0.232
- Space Group: P 64
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.527 | α = 90 |
| b = 99.527 | β = 90 |
| c = 73.695 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHENIX | phasing |
| Coot | model building |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2020-04-01
- Released Date: 2020-12-16 Deposition Author(s): Litzau, L.A., Tompkins, K., Shi, K., Nelson, A., Evans III, R.L., Gordon, W.R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM119483 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM118047 |
