8HGD | pdb_00008hgd

Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei

• PDB DOI: https://doi.org/10.2210/pdb8HGD/pdb

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


• Deposited: 2022-11-14 Released: 2023-11-22 
• Deposition Author(s): Jiang, Y., Cong, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei

Jiang, Y., Cong, Z.

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: 55.99 kDa 
• Atom Count: 3,877 
• Modeled Residue Count: 419 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MOH	C [auth B]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.15	α = 90
b = 103.369	β = 112.28
c = 52.489	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Jiang, Y., Cong, Z.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21977104

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release