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Download EndnoteHigh-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase
Fukuda, Y., Hirano, Y., Kusaka, K., Inoue, T., Tamada, T.(2020) Proc.Natl.Acad.Sci.USA --: --
6L46
High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans
- DOI: 10.2210/pdb6L46/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Geobacillus thermodenitrificans
- Expression System: Escherichia coli BL21(DE3)
- Deposited: 2019-10-16 Released: 2020-02-12
- Funding Organization(s): Japan Society for the Promotion of Science
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.3 Å
- R-Value Free: 0.112
- R-Value Work: 0.097
- Method: NEUTRON DIFFRACTION
- Resolution: 1.5 Å
- R-Value Free: 0.159
- R-Value Work: 0.142
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Copper-containing nitrite reductase | A | 323 | Geobacillus thermodenitrificans | Mutation(s): 0 Gene Names: nirK EC: 1.7.2.1 |
Find proteins for A0A1W6VP04 (Geobacillus thermodenitrificans) Go to UniProtKB: A0A1W6VP04 | ||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | A | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | A | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| CU Query on CU | A | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | Ligand Interaction | |
| MPD Query on MPD | A | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | Ligand Interaction | |
| DOD Query on DOD | A | DEUTERATED WATER D2 O XLYOFNOQVPJJNP-ZSJDYOACSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.3 Å
- R-Value Free: 0.112
- R-Value Work: 0.097
- Space Group: H 3
- Diffraction Data DOI:
10.18430/m36l46 Protein Diffraction
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 114.212 | α = 90.00 |
| b = 114.212 | β = 90.00 |
| c = 83.688 | γ = 120.00 |
- Method: NEUTRON DIFFRACTION
- Resolution: 1.5 Å
- R-Value Free: 0.159
- R-Value Work: 0.142
- Diffraction Data DOI:
10.18430/m36l46 Protein Diffraction
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| STARGazer | data reduction |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2019-10-16
- Released Date: 2020-02-12
- Deposition Author(s): Fukuda, Y., Hirano, Y., Kusaka, K., Inoue, T., Tamada, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science | Japan | -- |
