Download MendeleyActive site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues
Golan, G., Zharkov, D.O., Grollman, A.P., Shoham, G.To be published.
2OPF
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate
- PDB DOI: https://doi.org/10.2210/pdb2OPF/pdb
- NAKB: 2OPF
- Classification: HYDROLASE/DNA
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-01-29 Released: 2008-02-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.267
- R-Value Work: 0.240
- R-Value Observed: 0.240
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Endonuclease VIII | C [auth A] | 262 | Escherichia coli | Mutation(s): 1 Gene Names: nei EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data) |  |
UniProt | |||||
Find proteins for P50465 (Escherichia coli (strain K12)) Explore P50465 Go to UniProtKB: P50465 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P50465 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3' | A [auth B] | 12 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | B [auth C] | 12 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth C], G [auth A], H [auth A], I [auth A], J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.267
- R-Value Work: 0.240
- R-Value Observed: 0.240
- Space Group: P 43 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.556 | α = 90 |
| b = 73.556 | β = 90 |
| c = 170.113 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2008-02-26 Deposition Author(s): Golan, G., Zharov, D.O., Grollman, A.P., Shoham, G.
Revision History (Full details and data files)
- Version 1.0: 2008-02-26
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2021-11-10
Changes: Database references, Derived calculations - Version 1.3: 2023-10-25
Changes: Data collection, Refinement description
