Download MendeleyStructure characterization of sugar aminotransferases CalS13 and WecE provides the basis for a unifying structural model for stereochemical outcome.
Wang, F., Singh, S., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.To be published.
4ZAS | pdb_00004zas
Crystal structure of sugar aminotransferase CalS13 from Micromonospora echinospora
- PDB DOI: https://doi.org/10.2210/pdb4ZAS/pdb
- Entry: 4ZAS supersedes: 4YTJ
- Classification: TRANSFERASE
- Organism(s): Micromonospora echinospora
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-04-13 Released: 2015-04-29
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.47 Å
- R-Value Free: 0.229 (Depositor), 0.230 (DCC)
- R-Value Work: 0.173 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.174 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 2.2 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 |
| CalS13 | 404 | Micromonospora echinospora | Mutation(s): 0 Gene Names: calS13 |  | |
UniProt | |||||
Find proteins for Q8KND8 (Micromonospora echinospora) Explore Q8KND8 Go to UniProtKB: Q8KND8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8KND8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| T46 Query on T46 | H [auth B] | dTDP-4-keto-6-deoxyglucose C16 H24 N2 O15 P2 PSXWNITXWWECNY-UCBTUHGZSA-N |  | ||
| TYD Query on TYD | J [auth D], K [auth E], L [auth F] | THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N |  | ||
| SO4 Query on SO4 | G [auth B], I [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A, B, C, D, E A, B, C, D, E, F | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.47 Å
- R-Value Free: 0.229 (Depositor), 0.230 (DCC)
- R-Value Work: 0.173 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.174 (Depositor)
Diffraction Data: https://doi.org/10.18430/m34zas
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 71.57 | α = 90 |
| b = 88.74 | β = 96.22 |
| c = 189.81 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-04-29 Deposition Author(s): Wang, F., Singh, S., Miller, M.D., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
- This entry supersedes: 4YTJ
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | U01GM098248 |
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | CA84374 |
Revision History (Full details and data files)
- Version 1.0: 2015-04-29
Type: Initial release - Version 2.0: 2017-09-06
Changes: Author supporting evidence, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary - Version 2.1: 2019-12-04
Changes: Author supporting evidence - Version 2.2: 2025-04-02
Changes: Data collection, Database references, Structure summary
