4N17

Crystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, With bound beta-D-galacturonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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
TRAP dicarboxylate transporter, DctP subunit335Burkholderia ambifaria AMMDMutation(s): 0 
Gene Names: Bamb_6123
UniProt
Find proteins for Q0B2F6 (Burkholderia ambifaria (strain ATCC BAA-244 / DSM 16087 / CCUG 44356 / LMG 19182 / AMMD))
Explore Q0B2F6 
Go to UniProtKB:  Q0B2F6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0B2F6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.152α = 90
b = 101.369β = 90
c = 55.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Non-polymer description
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary