6ESU | pdb_00006esu

Artificial imine reductase mutant S112A-N118P-K121A-S122M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.211 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Directed Evolution of an Artificial Imine Reductase.

Hestericova, M.Heinisch, T.Alonso-Cotchico, L.Marechal, J.D.Vidossich, P.Ward, T.R.

(2018) Angew Chem Int Ed Engl 57: 1863-1868

  • DOI: https://doi.org/10.1002/anie.201711016
  • Primary Citation Related Structures: 
    6ESS, 6ESU

  • PubMed Abstract: 

    Artificial metalloenzymes, resulting from incorporation of a metal cofactor within a host protein, have received increasing attention in the last decade. The directed evolution is presented of an artificial transfer hydrogenase (ATHase) based on the biotin-streptavidin technology using a straightforward procedure allowing screening in cell-free extracts. Two streptavidin isoforms were yielded with improved catalytic activity and selectivity for the reduction of cyclic imines. The evolved ATHases were stable under biphasic catalytic conditions. The X-ray structure analysis reveals that introducing bulky residues within the active site results in flexibility changes of the cofactor, thus increasing exposure of the metal to the protein surface and leading to a reversal of enantioselectivity. This hypothesis was confirmed by a multiscale approach based mostly on molecular dynamics and protein-ligand dockings.


  • Organizational Affiliation
    • Department Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4002, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 18.02 kDa 
  • Atom Count: 1,002 
  • Modeled Residue Count: 123 
  • Deposited Residue Count: 159 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Streptavidin159Streptomyces avidiniiMutation(s): 4 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6IR

Query on 6IR



Download:Ideal Coordinates CCD File
B [auth A]5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[4-(2-azanylethylsulfamoyl)phenyl]pentanamide
C18 H27 N5 O4 S2
ZDLCBMIPYXADBN-ZOBUZTSGSA-N
IR

Query on IR



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.211 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.801α = 90
b = 57.801β = 90
c = 178.273γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description