9QGB | pdb_00009qgb

Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 (engineered Loop Swap from Achromobacter sp. JA81)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.161 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.130 (Depositor), 0.130 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QGB

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Rational Introduction of Electrostatic Interactions at Crystal Contacts to Enhance Protein Crystallization of an Ene Reductase.

Walla, B.Maslakova, A.Bischoff, D.Janowski, R.Niessing, D.Weuster-Botz, D.

(2025) Biomolecules 15

  • DOI: https://doi.org/10.3390/biom15040467
  • Primary Citation Related Structures: 
    9QGB, 9QGC, 9QGD, 9QGE, 9QGF

  • PubMed Abstract: 

    Protein crystallization is an alternative to well-established but cost-intensive and time-consuming chromatography in biotechnological processes, with protein crystallization defined as an essential unit operation for isolating proteins, e.g., active pharmaceutical ingredients. Crystalline therapeutic proteins attract interest in formulation and delivery processes of biopharmaceuticals due to the high purity, concentration, and stability of the crystalline state. Although improving protein crystallization is mainly achieved by high-throughput screening of crystallization conditions, recent studies have established a rational protein engineering approach to enhance crystallization for two homologous alcohol dehydrogenases from Lactobacillus brevis ( Lb ADH) and Lactobacillus kefiri ( Lk ADH). As generalizing crystallization processes across a wide range of target proteins remains challenging, this study takes a further step by applying the successful crystal contact engineering strategies for Lb ADH/ Lk ADH to a non-homologous protein, an NADH-binding derivative of the Nostoc sp. PCC 1720 ene reductase ( Nsp ER1-L1,5). Here, the focus lies on introducing electrostatic interactions at crystal contacts, specifically between lysine and glutamic acid. Out of the nine tested Nsp ER1-L1,5 mutants produced in E. coli , six crystallized, while four mutants revealed an increased propensity to crystallize in static µL-batch crystallization compared to the wild type: Q204K, Q350K, D352K, and T354K. The best-performing mutant Q204K was selected for upscaling, crystallizing faster than the wild type in a stirred batch crystallizer. Even when spiked with E. coli cell lysate, the mutant maintained increased crystallizability compared to the wild type. The results of this study highlight the potential of crystal contact engineering as a reliable tool for improving protein crystallization as an alternative to chromatography, paving the way for more efficient biotechnological downstream processing.


  • Organizational Affiliation
    • Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany.

Macromolecule Content 

  • Total Structure Weight: 83.66 kDa 
  • Atom Count: 7,065 
  • Modeled Residue Count: 714 
  • Deposited Residue Count: 750 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
All1865 protein
A, B
375Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: all1865
UniProt
Find proteins for A0ACD6B956 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore A0ACD6B956 
Go to UniProtKB:  A0ACD6B956
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B956
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
D [auth A],
M [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
E [auth A]
G [auth A]
H [auth A]
I [auth A]
C [auth A],
E [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
P [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
Z [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
Y [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.161 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.22α = 90
b = 67.78β = 93.52
c = 91.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWE2715/14-2

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references