Download MendeleySrtF sortase from Corynebacterium diphtheriae
Osipiuk, J., Gornicki, P., Ton-That, H., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)To be published.
5UUS
SrtF sortase from Corynebacterium diphtheriae
- PDB DOI: https://doi.org/10.2210/pdb5UUS/pdb
- Classification: HYDROLASE
- Organism(s): Corynebacterium diphtheriae NCTC 13129
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2017-02-17 Released: 2017-03-22
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.02 Å
- R-Value Free: 0.191
- R-Value Work: 0.164
- R-Value Observed: 0.165
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Possible sortase-like protein | A, B | 229 | Corynebacterium diphtheriae NCTC 13129 | Mutation(s): 0 Gene Names: DIP2272 |  |
UniProt | |||||
Find proteins for Q6NEK1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEK1 Go to UniProtKB: Q6NEK1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6NEK1 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | C [auth A], D [auth A], I [auth B], J [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | Ligand Interaction | |
| EDO Query on EDO | G [auth A], M [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| ACT Query on ACT | F [auth A], L [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | Ligand Interaction | |
| FMT Query on FMT | H [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | E [auth A], K [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 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: 2.02 Å
- R-Value Free: 0.191
- R-Value Work: 0.164
- R-Value Observed: 0.165
- Space Group: P 32 2 1
- Diffraction Data: https://doi.org/10.18430/M35UUS
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 69.99 | α = 90 |
| b = 69.99 | β = 90 |
| c = 237.292 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data scaling |
| HKL-3000 | data reduction |
| HKL-3000 | phasing |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-03-22 Deposition Author(s): Osipiuk, J., Gornicki, P., Ton-That, H., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272200700058C |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201200026C |
Revision History (Full details and data files)
- Version 1.0: 2017-03-22
Type: Initial release - Version 1.1: 2017-09-27
Changes: Author supporting evidence, Refinement description - Version 1.2: 2019-12-11
Changes: Author supporting evidence
