Download MendeleyStructural evidence of the flexibility of the CuM site
Fukuda, Y., Inoue, T.To be published.
3X1F
H294M mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans
- PDB DOI: https://doi.org/10.2210/pdb3X1F/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Geobacillus thermodenitrificans NG80-2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2014-11-16 Released: 2015-11-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.115
- R-Value Work: 0.092
- R-Value Observed: 0.093
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: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nitrite reductase | 352 | Geobacillus thermodenitrificans NG80-2 | Mutation(s): 1 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 | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | K [auth A], L [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| CU Query on CU | B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | I [auth A], J [auth A], M [auth A], N [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.115
- R-Value Work: 0.092
- R-Value Observed: 0.093
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.977 | α = 90 |
| b = 114.977 | β = 90 |
| c = 84.138 | 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: 2015-11-18 Deposition Author(s): Fukuda, Y., Inoue, T.
Revision History (Full details and data files)
- Version 1.0: 2015-11-18
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
