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)

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
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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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A368UNN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
DAO (Subject of Investigation/LOI) Query on DAO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.