3RWL

Structure of P450pyr hydroxylase

• PDB DOI: https://doi.org/10.2210/pdb3RWL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingopyxis macrogoltabida
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-05-09 Released: 2012-04-18 
• Deposition Author(s): Pompidor, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Evolving P450pyr hydroxylase for highly enantioselective hydroxylation at non-activated carbon atom.

Pham, S.Q., Pompidor, G., Liu, J., Li, X.D., Li, Z.

(2012) Chem Commun (Camb) 48: 4618-4620

• PubMed: 22430002 
• DOI: https://doi.org/10.1039/c2cc30779k
• Primary Citation of Related Structures:  
  3RWL


• PubMed Abstract: 
  

  Directed evolution of a monooxygenase to achieve very high enantioselectivity for hydroxylation at non-activated carbon atoms is demonstrated for the first time, where a triple mutant of P450pyr hydroxylase is obtained via determination of enzyme structure, iterative saturation mutagenesis, and high-throughput screening with a MS-based ee assay to increase the product ee from 53% to 98% for the hydroxylation of N-benzyl pyrrolidine to (S)-N-benzyl 3-hydroxypyrrolidine.

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Organizational Affiliation: 

Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 48.88 kDa 
• Atom Count: 3,617 
• Modelled Residue Count: 404 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 alkane hydroxylase 1 CYP153A7	A	426	Sphingopyxis macrogoltabida	Mutation(s): 0  Gene Names: ahpG1, Sphingomonas sp. EC: 1.14.15.3
UniProt
Find proteins for Q5F4D9 (Sphingopyxis macrogoltabida) Explore Q5F4D9  Go to UniProtKB:  Q5F4D9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.604	α = 90
b = 112.604	β = 90
c = 41.964	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Pompidor, G.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations