Download MendeleyStructure and Function of Copper Nitrite Reductase
Nojiri, M.(2016) Metalloenzymes In Denitrification: Applications And Environmental Impacts : 91-113
5B1J
Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin
- PDB DOI: https://doi.org/10.2210/pdb5B1J/pdb
- Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
- Organism(s): Achromobacter xylosoxidans, Hyphomicrobium denitrificans
- Mutation(s): No
- Deposited: 2015-12-04 Released: 2016-11-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.233
- R-Value Work: 0.171
- R-Value Observed: 0.175
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Copper-containing nitrite reductase | 336 | Achromobacter xylosoxidans | Mutation(s): 0 EC: 1.7.2.1 |  | |
UniProt | |||||
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Explore O68601 Go to UniProtKB: O68601 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O68601 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Blue copper protein | 124 | Hyphomicrobium denitrificans | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A7VL37 (Hyphomicrobium denitrificans) Explore A7VL37 Go to UniProtKB: A7VL37 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A7VL37 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CU Query on CU | D [auth A], E [auth A], F [auth B], G [auth B], H [auth C] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.233
- R-Value Work: 0.171
- R-Value Observed: 0.175
- Space Group: P 21 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 153.226 | α = 90 |
| b = 153.226 | β = 90 |
| c = 153.226 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-11-23 Deposition Author(s): Nojiri, M., Koteishi, H., Yoneda, R., Hira, D.
Revision History (Full details and data files)
- Version 1.0: 2016-11-23
Type: Initial release - Version 1.1: 2020-02-26
Changes: Data collection - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
