8YHN | pdb_00008yhn

Crystal structure of Cytochrome P450 107P2 from streptomyces avermitilis

• PDB DOI: https://doi.org/10.2210/pdb8YHN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces avermitilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-28 Released: 2025-03-05 
• Deposition Author(s): Jeong, E.S., Kim, V.C., Kim, C.M., Lee, Y.B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.229 (DCC) 

Starting Model: experimental

Literature

The crystal structure of substrate-free CYP107X1 from Streptomyces avermitilis

Xu, L.-H.

To be published.

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: 46.48 kDa 
• Atom Count: 3,084 
• Modeled Residue Count: 396 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	411	Streptomyces avermitilis	Mutation(s): 0  Gene Names: SAV14893_039980, SAV31267_046970
UniProt
Find proteins for Q82ES4 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82ES4  Go to UniProtKB:  Q82ES4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.229 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.128	α = 90
b = 66.44	β = 90
c = 111.756	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Jeong, E.S., Kim, V.C., Kim, C.M., Lee, Y.B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release