Download MendeleyStructural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI
Shen, B.W., Heiter, D., Xu, S., Stoddard, B.L.To be published.
8W2Q | pdb_00008w2q
8W2Q | pdb_00008w2q
BsaXI-DNA complex II
- PDB DOI: https://doi.org/10.2210/pdb8W2Q/pdb
- EM Map EMD-43755: EMDB EMDataResource
- NAKB: 8W2Q
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): Geobacillus stearothermophilus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-02-21 Released: 2024-10-30
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.06 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RM.BsaXI | 916 | Geobacillus stearothermophilus | Mutation(s): 0 Gene Names: E5Z46_18465 EC: 2.1.1.72 |  | |
Find similar proteins by:
| 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| S.BsaXI | 476 | Geobacillus stearothermophilus | Mutation(s): 0 Gene Names: GT3921_04730 |  | |
UniProt | |||||
Find proteins for A0A226QBA7 (Geobacillus thermocatenulatus) Explore A0A226QBA7 Go to UniProtKB: A0A226QBA7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A226QBA7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Find similar nucleic acids by: (by identity cutoff)
Sequence
Entity ID: 3 | ||||
| Molecule | Chains | Length | Organism | Image |
|---|---|---|---|---|
| DNA (41-MER) | 52 | Geobacillus stearothermophilus |  | |
Sequence AnnotationsExpand | ||||
Reference Sequence | ||||
Find similar nucleic acids by: (by identity cutoff)
Sequence
Entity ID: 4 | ||||
| Molecule | Chains | Length | Organism | Image |
|---|---|---|---|---|
| DNA (41-MER) | 52 | Geobacillus stearothermophilus |  | |
Sequence AnnotationsExpand | ||||
Reference Sequence | ||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAM Download:Ideal Coordinates CCD File | G [auth B] | S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N |  | ||
| SAH Download:Ideal Coordinates CCD File | F [auth A] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.06 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | 3.3 |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
Entry History
& Funding InformationDeposition Data
- Released Date: 2024-10-30 Deposition Author(s): Shen, B.W., Stoddard, B.L., Xu, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | Ro1-GM105691 |
Revision History (Full details and data files)
- Version 1.0: 2024-10-30
Type: Initial release
