8JRL

Crystal structure of P450 TleB with an indole alkaloid

• PDB DOI: https://doi.org/10.2210/pdb8JRL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces blastmyceticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-17 Released: 2024-04-17 
• Deposition Author(s): Wang, J., Yan, W.P.
• Funding Organization(s): Science and Technology Commission of Shanghai

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.208 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Regulation of P450 TleB catalytic flow for the synthesis of sulfur-containing indole alkaloids by substrate structure-directed strategy. and protein engineering.

Ge, X.Y., Long, Y., Wang, J., Gu, B., Yang, Z.X., Feng, Y.Y., Zheng, S., Li, Y.Y., Yan, W.P., Song, H.

(2023) Sci China B Chem 66: 3232-3241

• DOI: https://doi.org/10.1007/s11426-023-1755-4

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: 47.96 kDa 
• Atom Count: 3,410 
• Modelled Residue Count: 392 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P-450	A	418	Streptomyces blastmyceticus	Mutation(s): 0  Gene Names: tleB
UniProt
Find proteins for A0A077KEB8 (Streptomyces blastmyceticus) Explore A0A077KEB8  Go to UniProtKB:  A0A077KEB8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
V3X (Subject of Investigation/LOI)	C [auth A]	(2~{S})-~{N}-[(2~{S})-1-(4-fluoranyl-1~{H}-indol-3-yl)-3-oxidanyl-propan-2-yl]-3-methyl-2-sulfanyl-butanamide C16 H21 F N2 O2 S KKPTZRIROSBPNX-NHYWBVRUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.208 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.035	α = 90
b = 85.587	β = 90
c = 113.755	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Wang, J., Yan, W.P.

---

Funding Organization	Location	Grant Number
Science and Technology Commission of Shanghai	China	21ZR1433700

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release