5FYG | pdb_00005fyg

Structure of CYP153A from Marinobacter aquaeolei in complex with hydroxydodecanoic acid

• PDB DOI: https://doi.org/10.2210/pdb5FYG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Marinobacter nauticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2017-01-18 
• Deposition Author(s): Danesh-Azari, H.-R., Spandolf, C., Hoffman, S.M., Weissenborn, M., Hauer, B., Grogan, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids

Hoffman, S.M., Danesh Azari, H.-R., Spandolf, C., Weissenborn, M., Grogan, G., Hauer, B.

(2016) ChemCatChem 

• DOI: https://doi.org/10.1002/cctc.201600680

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 109.7 kDa 
• Atom Count: 7,014 
• Modeled Residue Count: 841 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450	A, B	470	Marinobacter nauticus	Mutation(s): 0
UniProt
Find proteins for A1TY82 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8)) Explore A1TY82  Go to UniProtKB:  A1TY82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
12H	D [auth A], F [auth B]	12-HYDROXYDODECANOIC ACID C12 H24 O3 ZDHCZVWCTKTBRY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.02	α = 90
b = 71.31	β = 90
c = 213.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Danesh-Azari, H.-R., Spandolf, C., Hoffman, S.M., Weissenborn, M., Hauer, B., Grogan, G.

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description