9DA9 | pdb_00009da9

Crystal structure of GluN1/GluN2A agonist-binding domains in complex with 7CKA and glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A galactose-based auto-expression system improves T7-inducible protein production in Escherichia coli.

Bosco, J.Gagliano, E.Boshae, K.L.Statz, J.P.Wheeler, T.B.Cuello, D.Sliter, A.Newby, C.Lin, B.Demeler, A.Pierpont, C.L.Yates-Hansen, C.Sydor, M.J.Ferrini, M.E.Kuch, K.C.Cooper, B.S.Piggott, B.J.Certel, S.J.Hansen, K.B.Sprang, S.R.Bowler, B.McClelland, L.Berkmen, M.Voronina, E.

(2025) Sci Rep 15: 8936-8936

  • DOI: https://doi.org/10.1038/s41598-025-91954-5
  • Primary Citation of Related Structures:  
    9DA9

  • PubMed Abstract: 

    Protein production using Escherichia coli is a cornerstone of modern biotechnology. In this study, we developed a novel auto-expression medium to maximize protein production. Each E. coli strain tested was capable of auto-expression in response to galactose, including strains in which the endogenous lacZ had been disrupted. This provides key evidence that galactose can regulate the lac operon independent of known lac operon-regulated metabolism. The enhanced capabilities of the novel auto-expression medium were documented across protein production systems including (1) increased yields for routinely expressed proteins (e.g. eGFP), (2) improved expression of human cytochrome c within a dual expression system, (3) robust auto-expression in lacZ-deficient strains producing proteins with challenging disulfide bonds, and (4) reproducible 8-fold increase in SpCas9 yields, at ≥ 95% purity. This novel medium can streamline production and improve yields for routine as well as challenging proteins, accelerating recombinant protein production and creating new opportunities in biotechnology and structural biology.


  • Organizational Affiliation
    • Division of Biological Sciences, Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, Center for Structural and Functional Neuroscience, Center for Environmental Health Sciences, University of Montana, Missoula, MT, 59812, USA. james.bosco@umontana.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1292Rattus norvegicusMutation(s): 0 
Gene Names: Grin1Glurz1
UniProt
Find proteins for P35439 (Rattus norvegicus)
Explore P35439 
Go to UniProtKB:  P35439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35439
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2A283Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus)
Explore Q00959 
Go to UniProtKB:  Q00959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00959
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.244α = 90
b = 87.338β = 90
c = 135.896γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

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 Neurological Disorders and Stroke (NIH/NINDS)United StatesNS097536
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS116055
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140963
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM109053

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references
  • Version 1.2: 2025-04-16
    Changes: Database references