Download MendeleyCopper inactivates DcsB by oxidizing the metal ligand Cys86 to sulfinic acid.
Oda, K., Matoba, Y.(2024) FEBS J
9IXD
Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
- PDB DOI: https://doi.org/10.2210/pdb9IXD/pdb
- Entry: 9IXD supersedes: 8IUW
- Classification: HYDROLASE
- Organism(s): Streptomyces lavendulae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-07-27 Released: 2024-11-20
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.205
- R-Value Work: 0.168
- R-Value Observed: 0.170
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| N(omega)-hydroxy-L-arginine amidinohydrolase | 281 | Streptomyces lavendulae | Mutation(s): 0 Gene Names: dcsB EC: 3.5.3.25 |  | |
UniProt | |||||
Find proteins for D2Z025 (Streptomyces lavendulae) Explore D2Z025 Go to UniProtKB: D2Z025 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D2Z025 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CU1 Query on CU1 | G [auth B] | COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N |  | ||
| CU (Subject of Investigation/LOI) Query on CU | F [auth B] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
| MN (Subject of Investigation/LOI) Query on MN | C [auth A], D [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| MG (Subject of Investigation/LOI) Query on MG | E [auth A], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSD Query on CSD | A, B | L-PEPTIDE LINKING | C3 H7 N O4 S |  | CYS |
| CSO Query on CSO | A, B | L-PEPTIDE LINKING | C3 H7 N O3 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.205
- R-Value Work: 0.168
- R-Value Observed: 0.170
- Space Group: P 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 46.4 | ¦Á = 83.69 |
| b = 47.145 | ¦Â = 84.7 |
| c = 59.393 | ¦Ă = 70.27 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-11-20 Deposition Author(s): Oda, K., Matoba, Y.
- This entry supersedes: 8IUW
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-11-20
Type: Initial release
