8HNJ | pdb_00008hnj

Domain-stabilized glutamine-binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Domain-wise dissection of thermal stability enhancement in multidomain proteins.

Oh, J.Durai, P.Kannan, P.Park, J.Yeon, Y.J.Lee, W.K.Park, K.Seo, M.H.

(2023) Int J Biol Macromol 237: 124141-124141

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.124141
  • Primary Citation Related Structures: 
    8HNJ

  • PubMed Abstract: 

    Stability is critical for the proper functioning of all proteins. Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering.


  • Organizational Affiliation
    • Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea.

Macromolecule Content 

  • Total Structure Weight: 154.13 kDa 
  • Atom Count: 10,642 
  • Modeled Residue Count: 1,314 
  • Deposited Residue Count: 1,380 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
A, B, C, D, E
A, B, C, D, E, F
230Escherichia coli 908519Mutation(s): 0 
Gene Names: HMPREF1604_05361
UniProt
Find proteins for P0AEQ3 (Escherichia coli (strain K12))
Explore P0AEQ3 
Go to UniProtKB:  P0AEQ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEQ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.1α = 90
b = 69.59β = 90.711
c = 83.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection