Download MendeleyCrystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA
Pastor, M., Czapinska, H., Lutz, T., Helbrecht, I., Xu, S., Bochtler, M.(2020) Nucleic Acids Res
6YJB
VcaM4I restriction endonuclease 5hmC-ssDNA complex
- DOI: 10.2210/pdb6YJB/pdb
- NDB: 6YJB
- Classification: HYDROLASE
- Organism(s): Vibrio campbellii, synthetic construct
- Expression System: Escherichia coli BL21(DE3), synthetic construct
- Mutation(s): No
- Deposited: 2020-04-02 Released: 2020-12-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.164
- R-Value Work: 0.142
- R-Value Observed: 0.144
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HNH endonuclease | A | 309 | Vibrio campbellii | Mutation(s): 0 Gene Names: DSB67_20905 |  |
Find proteins for A0A344KQF3 (Vibrio campbellii) Explore A0A344KQF3 Go to UniProtKB: A0A344KQF3 | |||||
Protein Feature ViewExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3') | B | 5 | synthetic construct |  | |
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | A, B | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| GOL Query on GOL | A, B | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | A | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.164
- R-Value Work: 0.142
- R-Value Observed: 0.144
- Space Group: P 62 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 128.685 | α = 90 |
| b = 128.685 | β = 90 |
| c = 110.895 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Deposited Date: 2020-04-02
- Released Date: 2020-12-23 Deposition Author(s): Pastor, M., Czapinska, H., Lutz, T., Helbrecht, I., Xu, S., Bochtler, M.
