Download MendeleyX-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine
Nakamura, R., Takahashi, Y., Fujishiro, T.To be published.
7XEQ | pdb_00007xeq
NifS with D-cysteine
- PDB DOI: https://doi.org/10.2210/pdb7XEQ/pdb
- Classification: BIOSYNTHETIC PROTEIN
- Organism(s): Helicobacter pylori
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2022-03-31 Released: 2023-04-05
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.225 (Depositor), 0.230 (DCC)
- R-Value Work: 0.181 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.183 (Depositor)
Starting Model: experimental
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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 |
| Cysteine desulfurase IscS | 401 | Helicobacter pylori | 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 | |
| 9YX (Subject of Investigation/LOI) Query on 9YX | D [auth A] | (2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid C11 H15 N2 O7 P S CXFXHBNEDOKOBZ-XCBNKYQSSA-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 |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.225 (Depositor), 0.230 (DCC)
- R-Value Work: 0.181 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.183 (Depositor)
Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 103.5 | α = 90 |
| b = 103.5 | β = 90 |
| c = 132.6 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-04-05 Deposition Author(s): Nakamura, R., Fujishiro, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 17K14510 |
Revision History (Full details and data files)
- Version 1.0: 2023-04-05
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
