5AEC | pdb_00005aec

Type II Baeyer-Villiger monooxygenase.The oxygenating constituent of 3,6-diketocamphane monooxygenase from CAM plasmid of Pseudomonas putida in complex with FMN.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.221 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The Oxygenating Constituent of 3,6-Diketocamphane Monooxygenase from the Cam Plasmid of Pseudomonas Putida: The First Crystal Structure of a Type II Baeyer-Villiger Monooxygenase.

Isupov, M.N.Schroder, E.Gibson, R.P.Beecher, J.Donadio, G.Saneei, V.Dcunha, S.A.Mcghie, E.J.Sayer, C.Davenport, C.F.Lau, P.C.Hasegawa, Y.Iwaki, H.Kadow, M.Balke, K.Bornscheuer, U.T.Bourenkov, G.Littlechild, J.A.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2344

  • DOI: https://doi.org/10.1107/S1399004715017939
  • Primary Citation Related Structures: 
    4UWM, 5AEC

  • PubMed Abstract: 

    The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.


  • Organizational Affiliation
    • The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England.

Macromolecule Content 

  • Total Structure Weight: 86.87 kDa 
  • Atom Count: 7,173 
  • Modeled Residue Count: 728 
  • Deposited Residue Count: 756 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3,6-DIKETOCAMPHANE 1,6 MONOOXYGENASE
A, B
378Pseudomonas putidaMutation(s): 0 
EC: 1.14.13 (PDB Primary Data), 1.14.14.155 (UniProt)
UniProt
Find proteins for D7UER1 (Pseudomonas putida)
Explore D7UER1 
Go to UniProtKB:  D7UER1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7UER1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIN

Query on PIN



Download:Ideal Coordinates CCD File
C [auth A],
M [auth B]
PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
C8 H18 N2 O6 S2
IHPYMWDTONKSCO-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
T [auth B],
U [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
V [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.221 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.963α = 90
b = 93.317β = 90
c = 161.893γ = 90
Software Package:
Software NamePurpose
CCP4model building
Aimlessdata scaling
MOLREPphasing
MLPHAREphasing
DMphasing
CCP4phasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description