3BUJ | pdb_00003buj

Crystal Structure of CalO2

• PDB DOI: https://doi.org/10.2210/pdb3BUJ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Micromonospora echinospora
• Expression System: Streptomyces lividans
• Mutation(s): No 


• Deposited: 2008-01-02 Released: 2008-04-29 
• Deposition Author(s): McCoy, J.G., Johnson, H.D., Singh, S., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of CalO2: a putative orsellinic acid P450 oxidase in the calicheamicin biosynthetic pathway.

McCoy, J.G., Johnson, H.D., Singh, S., Bingman, C.A., Lei, I.K., Thorson, J.S., Phillips Jr., G.N.

(2009) Proteins 74: 50-60

• PubMed: 18561189 
• DOI: https://doi.org/10.1002/prot.22131
• Primary Citation Related Structures: 
  3BUJ


• PubMed Abstract: 
  

  Although bacterial iterative Type I polyketide synthases are now known to participate in the biosynthesis of a small set of diverse natural products, the subsequent downstream modification of the resulting polyketide products remains poorly understood. Toward this goal, we report the X-ray structure determination at 2.5 A resolution and preliminary characterization of the putative orsellenic acid P450 oxidase (CalO2) involved in calicheamicin biosynthesis. These studies represent the first crystal structure for a P450 involved in modifying a bacterial iterative Type I polyketide product and suggest the CalO2-catalyzed step may occur after CalO3-catalyzed iodination and may also require a coenzyme A- (CoA) or acyl carrier protein- (ACP) bound substrate. Docking studies also reveal a putative docking site within CalO2 for the CLM orsellinic acid synthase (CalO5) ACP domain which involves a well-ordered helix along the CalO2 active site cavity that is unique compared with other P450 structures.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.

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: 44.59 kDa 
• Atom Count: 3,262 
• Modeled Residue Count: 397 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalO2	A	397	Micromonospora echinospora	Mutation(s): 0  Gene Names: calO2
UniProt
Find proteins for Q8KND6 (Micromonospora echinospora) Explore Q8KND6  Go to UniProtKB:  Q8KND6

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: 2.47 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.202	α = 90
b = 71.202	β = 90
c = 204.451	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): McCoy, J.G., Johnson, H.D., Singh, S., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N.

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2013-01-30
  Changes: Database references, Structure summary
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description