8RTV | pdb_00008rtv

Crystal structure of CYP154E1 from Thermobifida fusca YX in complex with 4-Phenylimidazole

• PDB DOI: https://doi.org/10.2210/pdb8RTV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-29 Released: 2025-02-12 
• Deposition Author(s): Bikbaev, K., Hoelzel, S., Urlacher, V., Span, I.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.271 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 

Starting Model: experimental

Literature

Structural determination of the CYP154E1 cytochrome P450 from Thermobifida fusca YX

Bikbaev, K., Hoelzel, S., Urlacher, V., Span, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 89.32 kDa 
• Atom Count: 6,540 
• Modeled Residue Count: 790 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450-family protein	A, B	395	Thermobifida fusca YX	Mutation(s): 0  Gene Names: Tfu_2976
UniProt
Find proteins for Q47KL3 (Thermobifida fusca (strain YX)) Explore Q47KL3  Go to UniProtKB:  Q47KL3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
231 (Subject of Investigation/LOI)	D [auth A], F [auth B]	4-PHENYL-1H-IMIDAZOLE C9 H8 N2 XHLKOHSAWQPOFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.334	α = 90
b = 97.176	β = 90
c = 135.688	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
MOLREP	phasing
Coot	model building
XDS	data reduction
BUCCANEER	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Bikbaev, K., Hoelzel, S., Urlacher, V., Span, I.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	031A223A

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release