Download MendeleyRadical Tropolone Biosynthesis
Doyon, T.J., Skinner, K., Yang, D., Mallik, L., Wymore, T., Koutmos, M., Zimmerman, P.M., Narayan, A.(2020) ChemRxiv
6XJJ | pdb_00006xjj
Structure of non-heme iron enzyme TropC: Radical tropolone biosynthesis
- PDB DOI: https://doi.org/10.2210/pdb6XJJ/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Talaromyces stipitatus ATCC 10500
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-06-24 Released: 2021-06-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.251 (Depositor), 0.250 (DCC)
- R-Value Work: 0.210 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.212 (Depositor)
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
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 2-oxoglutarate-dependent dioxygenase tropC | 358 | Talaromyces stipitatus ATCC 10500 | Mutation(s): 0 Gene Names: tropC, tsR5, TSTA_117800 EC: 1.14 |  | |
UniProt | |||||
Find proteins for B8M9K5 (Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006)) Explore B8M9K5 Go to UniProtKB: B8M9K5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B8M9K5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| YT3 Query on YT3 | C [auth A] | YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | D [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| FE Query on FE | B [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.251 (Depositor), 0.250 (DCC)
- R-Value Work: 0.210 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.212 (Depositor)
Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 111.014 | α = 90 |
| b = 111.014 | β = 90 |
| c = 89.889 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2021-06-02 Deposition Author(s): Mallik, L., Doyon, T.J., Narayan, A.R.H., Koutmos, M.
Revision History (Full details and data files)
- Version 1.0: 2021-06-02
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
