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.
7XEL
SufS soaked with D-penicillamine
- PDB DOI: https://doi.org/10.2210/pdb7XEL/pdb
- Classification: BIOSYNTHETIC PROTEIN
- Organism(s): Bacillus subtilis subsp. subtilis str. 168
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- 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: 1.80 Å
- R-Value Free: 0.188
- R-Value Work: 0.159
- R-Value Observed: 0.160
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
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 SufS | 419 | Bacillus subtilis subsp. subtilis str. 168 | Mutation(s): 0 Gene Names: sufS, csd, yurW, BSU32690 EC: 2.8.1.7 |  | |
UniProt | |||||
Find proteins for O32164 (Bacillus subtilis (strain 168)) Explore O32164 Go to UniProtKB: O32164 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O32164 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | C [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | D [auth A], E [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | B [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.188
- R-Value Work: 0.159
- R-Value Observed: 0.160
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93 | α = 90 |
| b = 93 | β = 90 |
| c = 129 | γ = 120 |
| 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 | 17K19340 |
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
