4PGN

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND INDOLE PYRUVATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

Vetting, M.W.Al-Obaidi, N.Zhao, S.San Francisco, B.Kim, J.Wichelecki, D.J.Bouvier, J.T.Solbiati, J.O.Vu, H.Zhang, X.Rodionov, D.A.Love, J.D.Hillerich, B.S.Seidel, R.D.Quinn, R.J.Osterman, A.L.Cronan, J.E.Jacobson, M.P.Gerlt, J.A.Almo, S.C.

(2015) Biochemistry 54: 909-931

  • DOI: https://doi.org/10.1021/bi501388y
  • Primary Citation of Related Structures:  
    4LN5, 4MCO, 4MEV, 4MHF, 4MIJ, 4MNC, 4MNI, 4MX6, 4N15, 4N17, 4N4U, 4N6D, 4N6K, 4N8G, 4N8Y, 4N91, 4NAP, 4NF0, 4NG7, 4NGU, 4NHB, 4NN3, 4NQ8, 4NX1, 4O7M, 4O8M, 4O94, 4OA4, 4OAN, 4OVP, 4OVQ, 4OVR, 4OVS, 4OVT, 4P1E, 4P1L, 4P3L, 4P47, 4P56, 4P8B, 4P9K, 4PAF, 4PAI, 4PAK, 4PBH, 4PBQ, 4PC9, 4PCD, 4PDD, 4PDH

  • PubMed Abstract: 

    The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular solute-binding protein, family 7
A, B, C, D
334Oleidesulfovibrio alaskensis G20Mutation(s): 0 
Gene Names: Dde_0634
UniProt
Find proteins for Q315G1 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20))
Explore Q315G1 
Go to UniProtKB:  Q315G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ315G1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3IO
Query on 3IO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID
C11 H9 N O3
RSTKLPZEZYGQPY-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
K [auth C],
L [auth C],
N [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.122α = 90
b = 144.459β = 90.33
c = 95.466γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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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 StatesGM093342

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2015-10-14
    Changes: Data collection
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2023-12-27
    Changes: Data collection, Database references