Download MendeleyK2U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
Lee, I.H., Ho, T.H., Kang, L.W.To be published.
6JFQ
K2U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
- PDB DOI: https://doi.org/10.2210/pdb6JFQ/pdb
- Classification: HYDROLASE
- Organism(s): Staphylococcus aureus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2019-02-11 Released: 2020-02-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.252
- R-Value Work: 0.208
- R-Value Observed: 0.210
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 |
| Peptide deformylase | 184 | Staphylococcus aureus | Mutation(s): 0 Gene Names: def, def1, pdf1 EC: 3.5.1.88 |  | |
UniProt | |||||
Find proteins for P68826 (Staphylococcus aureus) Explore P68826 Go to UniProtKB: P68826 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P68826 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| K2U Query on K2U | C [auth A] | (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid C18 H20 O3 S OBXQOECJZPGJTO-SJLPKXTDSA-N |  | ||
| NI Query on NI | B [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.252
- R-Value Work: 0.208
- R-Value Observed: 0.210
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 95.429 | α = 90 |
| b = 120.699 | β = 90 |
| c = 47.12 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data scaling |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2020-02-12 Deposition Author(s): Lee, I.H., Ho, T.H., Kang, L.W.
Revision History (Full details and data files)
- Version 1.0: 2020-02-12
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
