Download MendeleyDehaloperoxidase B from Amphitrite ornata: benzimidazole complex
Moreno Chicano, T., Hough, M.A.To be published.
5K1L
Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex
- PDB DOI: https://doi.org/10.2210/pdb5K1L/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Amphitrite ornata
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-05-18 Released: 2017-06-07
- Funding Organization(s): Leverhulme Trust, National Science Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.08 Å
- R-Value Free: 0.177
- R-Value Work: 0.151
- R-Value Observed: 0.152
Starting Model: experimental
View more details
This is version 1.2 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 |
| Dehaloperoxidase B | 137 | Amphitrite ornata | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7 Go to UniProtKB: Q9NAV7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NAV7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on HEM | C [auth A], F [auth B] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| BZI Query on BZI | D [auth A], G [auth B] | BENZIMIDAZOLE C7 H6 N2 HYZJCKYKOHLVJF-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | E [auth A], H [auth B], I [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.08 Å
- R-Value Free: 0.177
- R-Value Work: 0.151
- R-Value Observed: 0.152
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 60.79 | α = 90 |
| b = 68.3 | β = 90 |
| c = 68.53 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Aimless | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-06-07 Deposition Author(s): Moreno Chicano, T., Hough, M.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Leverhulme Trust | United Kingdom | RPG-2014-355 |
| National Science Foundation | United States | CHE-1150709 |
Revision History (Full details and data files)
- Version 1.0: 2017-06-07
Type: Initial release - Version 1.1: 2018-12-19
Changes: Author supporting evidence, Data collection, Database references, Derived calculations - Version 1.2: 2024-01-10
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
