7TNB | pdb_00007tnb

Caulobacter segnis arene reductase (CSAR) - WT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.186 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.168 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TNB

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

An asymmetric sp 3 -sp 3 cross-electrophile coupling using 'ene'-reductases.

Fu, H.Cao, J.Qiao, T.Qi, Y.Charnock, S.J.Garfinkle, S.Hyster, T.K.

(2022) Nature 610: 302-307

  • DOI: https://doi.org/10.1038/s41586-022-05167-1
  • Primary Citation Related Structures: 
    7TNB

  • PubMed Abstract: 

    The catalytic asymmetric construction of Csp 3 -Csp 3 bonds remains one of the foremost challenges in organic synthesis 1 . Metal-catalysed cross-electrophile couplings (XECs) have emerged as a powerful tool for C-C bond formation 2-5 . However, coupling two distinct Csp 3 electrophiles with high cross-selectivity and stereoselectivity continues as an unmet challenge. Here we report a highly chemoselective and enantioselective Csp 3 -Csp 3 XEC between alkyl halides and nitroalkanes catalysed by flavin-dependent 'ene'-reductases (EREDs). Photoexcitation of the enzyme-templated charge-transfer complex between an alkyl halide and a flavin cofactor enables the chemoselective reduction of alkyl halide over the thermodynamically favoured nitroalkane partner. The key C-C bond-forming step occurs by means of the reaction of an alkyl radical with an in situ-generated nitronate to form a nitro radical anion that collapses to form nitrite and an alkyl radical. An enzyme-controlled hydrogen atom transfer (HAT) affords high levels of enantioselectivity. This reactivity is unknown in small-molecule catalysis and highlights the potential for enzymes to use new mechanisms to address long-standing synthetic challenges.


  • Organizational Affiliation
    • Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 40.57 kDa 
  • Atom Count: 3,099 
  • Modeled Residue Count: 353 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:flavin oxidoreductase/NADH oxidaseA [auth AAA]366Caulobacter segnisMutation(s): 0 
Gene Names: Cseg_1902
UniProt
Find proteins for D5VJG6 (Caulobacter segnis (strain ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059))
Explore D5VJG6 
Go to UniProtKB:  D5VJG6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5VJG6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
H [auth AAA]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth AAA]
C [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
B [auth AAA],
C [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
M [auth AAA]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.186 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.168 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.47α = 90
b = 104.175β = 90
c = 144.328γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127703-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description