1N5T | pdb_00001n5t

Crystal structure of a Monooxygenase from the gene ActVA-Orf6 of Streptomyces coelicolor in complex with the ligand Oxidized Acetyl Dithranol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.256 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis

Sciara, G.Kendrew, S.G.Miele, A.E.Marsh, N.G.Federici, L.Malatesta, F.Schimperna, G.Savino, C.Vallone, B.

(2003) EMBO J 22: 205-215

  • DOI: https://doi.org/10.1093/emboj/cdg031
  • Primary Citation Related Structures: 
    1LQ9, 1N5Q, 1N5S, 1N5T, 1N5V

  • PubMed Abstract: 

    ActVA-Orf6 monooxygenase from Streptomyces coelicolor that catalyses the oxidation of an aromatic intermediate of the actinorhodin biosynthetic pathway is a member of a class of small monooxygenases that carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The overall structure is a ferredoxin-like fold with a novel dimeric assembly, indicating that the widely represented ferredoxin fold may sustain yet another functionality. The resolution (1.3 A) of the enzyme structure and its complex with substrate and product analogues allows us to visualize the mechanism of binding and activation of the substrate for attack by molecular oxygen, and utilization of two gates for the reaction components including a proton gate and an O(2)/H(2)O gate with a putative protein channel. This is the first crystal structure of an enzyme involved in the tailoring of a type II aromatic polyketide and illustrates some of the enzyme-substrate recognition features that may apply to a range of other enzymes involved in modifying a polyketide core structure.


  • Organizational Affiliation
    • Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, Università di Roma 'La Sapienza', Piazzale A.Moro, 5, 00185 Roma, Italy.

Macromolecule Content 

  • Total Structure Weight: 24.26 kDa 
  • Atom Count: 1,835 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 224 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ActVA-Orf6 monooxygenase
A, B
112Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: ActVA-Orf6
UniProt
Find proteins for Q53908 (Streptomyces coelicolor)
Explore Q53908 
Go to UniProtKB:  Q53908
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53908
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OAL

Query on OAL



Download:Ideal Coordinates CCD File
C [auth B](1,8-DIHYDROXY-9,10-DIOXO-9,10-DIHYDRO-ANTHRACEN-2-YL)-ACETIC ACID
C16 H10 O6
IKFRFGXQHSBCQM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.256 (Depositor) 
  • R-Value Work:  0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.216α = 90
b = 59.974β = 90
c = 71.629γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description