9KKI | pdb_00009kki

Crystal structure of the CYP153A double mutant L354V/V456G from Marinobacter aquaeolei

• PDB DOI: https://doi.org/10.2210/pdb9KKI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Marinobacter nauticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-11-13 Released: 2025-11-19 
• Deposition Author(s): Qin, M.M., Jiang, Y.P., Cong, Z.Q., Zhao, P.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structure of the CYP153A double mutant L354V/V456G from Marinobacter aquaeolei at 2.20 Angstroms resolution

Qin, M.M., Jiang, Y.P., Cong, Z.Q., Zhao, P.X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 112.08 kDa 
• Atom Count: 7,272 
• Modeled Residue Count: 844 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B	480	Marinobacter nauticus	Mutation(s): 2  Gene Names: DET51_1164
UniProt
Find proteins for A0A368UNN3 (Marinobacter nauticus) Explore A0A368UNN3  Go to UniProtKB:  A0A368UNN3

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
DAO (Subject of Investigation/LOI)	D [auth A], F [auth B]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.315	α = 90
b = 100.49	β = 90
c = 223.068	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Qin, M.M., Jiang, Y.P., Cong, Z.Q., Zhao, P.X.

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

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release