Download MendeleyCrystallographic evidence for side-on dioxygen trapped on type 2 copper in copper-containing nitrite reductase
Fukuda, Y., Inoue, T.To be published.
3WNI
1.50 A resolution crystal structure of dioxygen bound copper-containing nitrite reductase from Geobacillus thermodenitrificans
- PDB DOI: https://doi.org/10.2210/pdb3WNI/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Geobacillus thermodenitrificans NG80-2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-12-10 Released: 2014-12-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.149
- R-Value Work: 0.108
- R-Value Observed: 0.110
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| Nitrite reductase | 323 | Geobacillus thermodenitrificans NG80-2 | Mutation(s): 0 Gene Names: nirK |  | |
UniProt | |||||
Find proteins for A4IL26 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IL26 Go to UniProtKB: A4IL26 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A4IL26 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | F [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| PEG Query on PEG | G [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| CU Query on CU | B [auth A], C [auth A], D [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | H [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| OXY Query on OXY | E [auth A] | OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.149
- R-Value Work: 0.108
- R-Value Observed: 0.110
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 115.017 | α = 90 |
| b = 115.017 | β = 90 |
| c = 84.543 | γ = 120 |
| Software Name | Purpose |
|---|---|
| BSS | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-12-10 Deposition Author(s): Fukuda, Y., Inoue, T.
Revision History (Full details and data files)
- Version 1.0: 2014-12-10
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
