Download MendeleyStructural snapshot of cysteine desulfurase NifS with L-cysteine in initiation of catalysis
Fujishiro, T., Nakamura, R., Takahashi, Y.To be published.
5WT6
Cysteine persulfide intermediate of NifS from Helicobacter pylori
- PDB DOI: https://doi.org/10.2210/pdb5WT6/pdb
- Classification: TRANSFERASE
- Organism(s): Helicobacter pylori 26695
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2016-12-09 Released: 2017-12-13
- Funding Organization(s): JSPS, the Sumitomo Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.30 Å
- R-Value Free: 0.245
- R-Value Work: 0.217
- R-Value Observed: 0.218
Starting Model: experimental
View more details
This is version 1.3 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 |
| Cysteine desulfurase IscS | 401 | Helicobacter pylori 26695 | Mutation(s): 2 Gene Names: iscS, HP_0220 EC: 2.8.1.7 |  | |
UniProt | |||||
Find proteins for O25008 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25008 Go to UniProtKB: O25008 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O25008 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PDA Query on PDA | D [auth A] | 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID C11 H17 N2 O7 P WACJCHFWJNNBPR-ZETCQYMHSA-N |  | ||
| IPA Query on IPA | B [auth A] | ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSS Query on CSS | A | L-PEPTIDE LINKING | C3 H7 N O2 S2 |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.30 Å
- R-Value Free: 0.245
- R-Value Work: 0.217
- R-Value Observed: 0.218
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 102.75 | α = 90 |
| b = 102.75 | β = 90 |
| c = 131.97 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-12-13 Deposition Author(s): Fujishiro, T., Nakamura, R., Takahashi, Y.
| Funding Organization | Location | Grant Number |
|---|---|---|
| JSPS | Japan | 15H04472 |
| JSPS | Japan | 15H06085 |
| the Sumitomo Foundation | Japan | 163037 |
Revision History (Full details and data files)
- Version 1.0: 2017-12-13
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2023-11-15
Changes: Data collection - Version 1.3: 2024-11-13
Changes: Structure summary
