Download MendeleyHoming endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s
Chang, C., Gao, Y.To be published.
8VNB
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 240s
- PDB DOI: https://doi.org/10.2210/pdb8VNB/pdb
- NAKB: 8VNB
- Classification: HYDROLASE/DNA
- Organism(s): synthetic construct, Physarum polycephalum
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-01-13 Released: 2024-07-10
- Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.72 Å
- R-Value Free: 0.197
- R-Value Work: 0.177
- R-Value Observed: 0.178
Starting Model: experimental
View more details
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) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Intron-encoded endonuclease I-PpoI | E [auth A], F [auth B] | 162 | Physarum polycephalum | Mutation(s): 0 EC: 3.1 |  |
UniProt | |||||
Find proteins for Q94702 (Physarum polycephalum) Explore Q94702 Go to UniProtKB: Q94702 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q94702 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3') | A [auth C], C [auth D] | 13 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3') | B [auth c], D [auth d] | 8 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | G [auth C], H [auth D], L [auth A], M [auth A], Q [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | I [auth A], J [auth A], N [auth B], O [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG (Subject of Investigation/LOI) Query on MG | K [auth A], P [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.72 Å
- R-Value Free: 0.197
- R-Value Work: 0.177
- R-Value Observed: 0.178
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 113.65 | α = 90 |
| b = 113.65 | β = 90 |
| c = 88.31 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Cancer Prevention and Research Institute of Texas (CPRIT) | United States | RR190046 |
| Welch Foundation | United States | C-2033-20200401 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | T32 GM008280 |
Revision History (Full details and data files)
- Version 1.0: 2024-07-10
Type: Initial release - Version 1.1: 2024-07-17
Changes: Derived calculations
