7Y9O

Crystal structure of a CYP109B4 variant from Bacillus sonorensis

• PDB DOI: https://doi.org/10.2210/pdb7Y9O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus sonorensis L12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-06-25 Released: 2023-05-03 
• Deposition Author(s): Shen, P.P., Huang, J.-W., Li, X., Liu, W.D., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.222 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Rationally Controlling Selective Steroid Hydroxylation via Scaffold Sampling of a P450 Family

Zhang, X., Shen, P., Zhao, J., Chen, Y., Li, X., Huang, J.W., Zhang, L., Li, Q., Gao, C., Xing, Q., Chen, C.C., Guo, R.T., Li, A.

(2023) ACS Catal 13: 1280-1289

• DOI: https://doi.org/10.1021/acscatal.2c04906

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 47.27 kDa 
• Atom Count: 3,691 
• Modelled Residue Count: 390 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 monooxygenase YjiB	A	406	Bacillus sonorensis L12	Mutation(s): 10  Gene Names: BSONL12_06623
UniProt
Find proteins for M5PFT9 (Bacillus sonorensis L12) Explore M5PFT9  Go to UniProtKB:  M5PFT9

Small Molecules

Ligands 3 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
IMD (Subject of Investigation/LOI)	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.222 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.87	α = 90
b = 62.602	β = 90
c = 140.526	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Shen, P.P., Huang, J.-W., Li, X., Liu, W.D., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description