6MYW | pdb_00006myw

Gluconobacter Ene-Reductase (GluER) mutant - T36A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.145 (Depositor), 0.157 (DCC) 
  • R-Value Work: 
    0.123 (Depositor), 0.135 (DCC) 
  • R-Value Observed: 
    0.124 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Photoexcitation of flavoenzymes enables a stereoselective radical cyclization.

Biegasiewicz, K.F.Cooper, S.J.Gao, X.Oblinsky, D.G.Kim, J.H.Garfinkle, S.E.Joyce, L.A.Sandoval, B.A.Scholes, G.D.Hyster, T.K.

(2019) Science 364: 1166-1169

  • DOI: https://doi.org/10.1126/science.aaw1143
  • Primary Citation Related Structures: 
    6MYW, 6O08

  • PubMed Abstract: 

    Photoexcitation is a common strategy for initiating radical reactions in chemical synthesis. We found that photoexcitation of flavin-dependent "ene"-reductases changes their catalytic function, enabling these enzymes to promote an asymmetric radical cyclization. This reactivity enables the construction of five-, six-, seven-, and eight-membered lactams with stereochemical preference conferred by the enzyme active site. After formation of a prochiral radical, the enzyme guides the delivery of a hydrogen atom from flavin-a challenging feat for small-molecule chemical reagents. The initial electron transfer occurs through direct excitation of an electron donor-acceptor complex that forms between the substrate and the reduced flavin cofactor within the enzyme active site. Photoexcitation of promiscuous flavoenzymes has thus furnished a previously unknown biocatalytic reaction.


  • Organizational Affiliation
    • Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

Macromolecule Content 

  • Total Structure Weight: 164.59 kDa 
  • Atom Count: 13,184 
  • Modeled Residue Count: 1,424 
  • Deposited Residue Count: 1,476 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-ethylmaleimide reductase
A, B, C, D
369Gluconobacter oxydansMutation(s): 1 
Gene Names: noxAD934_01855AD950_09540
UniProt
Find proteins for A1E8I9 (Gluconobacter oxydans)
Explore A1E8I9 
Go to UniProtKB:  A1E8I9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1E8I9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
O [auth C],
Z [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth D]
DA [auth D]
G [auth A]
H [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
Y [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth D],
F [auth A],
J [auth B],
P [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth B]
N [auth B]
T [auth C]
U [auth C]
V [auth C]
M [auth B],
N [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.145 (Depositor), 0.157 (DCC) 
  • R-Value Work:  0.123 (Depositor), 0.135 (DCC) 
  • R-Value Observed: 0.124 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.475α = 90
b = 45.154β = 107.67
c = 163.744γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description