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 
• Deposition Author(s): Mallik, L., Doyon, T.J., Narayan, A.R.H., Koutmos, M.

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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

Literature

Radical Tropolone Biosynthesis

Doyon, T.J., Skinner, K., Yang, D., Mallik, L., Wymore, T., Koutmos, M., Zimmerman, P.M., Narayan, A.

(2020) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv.12780044.v1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.27 kDa 
• Atom Count: 2,319 
• Modeled Residue Count: 291 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate-dependent dioxygenase tropC	A	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YT3	C [auth A]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
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 Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description