8B2P | pdb_00008b2p

CYP153A71 from Acinetobacter dieselolei bound to octanoic acid

• PDB DOI: https://doi.org/10.2210/pdb8B2P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alloalcanivorax dieselolei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-14 Released: 2022-11-02 
• Deposition Author(s): Opperman, D.J., Tolmie, C.
• Funding Organization(s): Global Challenges Research Fund, National Research Foundation in South Africa, Department of Science and Innovation, South Africa

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.271 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

CYP153A71 from Alcanivorax dieselolei: Oxidation beyond Monoterminal Hydroxylation of n-Alkanes

Jacobs, C.L., do Aido-Machado, R., Tolmie, C., Smit, M.S., Opperman, D.J.

(2022) Catalysts 

• DOI: https://doi.org/10.3390/catal12101213

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 109.28 kDa 
• Atom Count: 7,280 
• Modeled Residue Count: 844 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 alkane hydroxylase	A, B	470	Alloalcanivorax dieselolei	Mutation(s): 0  Gene Names: p450
UniProt
Find proteins for D0Q1H3 (Alloalcanivorax dieselolei) Explore D0Q1H3  Go to UniProtKB:  D0Q1H3

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
OCA	D [auth A], F [auth B]	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.271 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.661	α = 90
b = 76.817	β = 90.53
c = 107.344	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Opperman, D.J., Tolmie, C.

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Funding Organization	Location	Grant Number
Global Challenges Research Fund	United Kingdom	ST/R002754/1
National Research Foundation in South Africa	South Africa	112094
Department of Science and Innovation, South Africa	South Africa	c*change, PAR-02

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description