Download MendeleyCrystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA in the presence of Mg2+
Shin, Y., Murakami, K.S.To be published.
7R8I
Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA in the presence of Mg2+
- PDB DOI: https://doi.org/10.2210/pdb7R8I/pdb
- NAKB: 7R8I
- Classification: HYDROLASE/DNA
- Organism(s): Pseudooceanicola lipolyticus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2021-06-26 Released: 2022-11-09
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.248
- R-Value Work: 0.213
- R-Value Observed: 0.214
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:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Argonaute | 789 | Pseudooceanicola lipolyticus | Mutation(s): 0 Gene Names: CVM52_05730 |  | |
UniProt | |||||
Find proteins for A0A2M8J4C7 (Pseudooceanicola lipolyticus) Explore A0A2M8J4C7 Go to UniProtKB: A0A2M8J4C7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2M8J4C7 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*TP*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A) | B [auth T] | 18 | Pseudooceanicola lipolyticus |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.248
- R-Value Work: 0.213
- R-Value Observed: 0.214
- Space Group: I 2 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 200.019 | α = 90 |
| b = 200.019 | β = 90 |
| c = 200.019 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-11-09 Deposition Author(s): Shin, Y., Murakami, K.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | -- |
Revision History (Full details and data files)
- Version 1.0: 2022-11-09
Type: Initial release
