4NF0

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOMONAS AERUGINOSA PAO1 (PA4616), TARGET EFI-510182, WITH BOUND L-Malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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
Probable c4-dicarboxylate-binding protein
A, B, C, D, E
A, B, C, D, E, F, G, H
339Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA4616
UniProt
Find proteins for Q9HVH5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVH5 
Go to UniProtKB:  Q9HVH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVH5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMR
Query on LMR

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
M [auth C]
O [auth D]
R [auth F]
I [auth A],
J [auth B],
M [auth C],
O [auth D],
R [auth F],
T [auth G],
U [auth H]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth B]
L [auth B]
N [auth C]
P [auth D]
Q [auth D]
K [auth B],
L [auth B],
N [auth C],
P [auth D],
Q [auth D],
S [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.959α = 99.01
b = 73.91β = 91.59
c = 122.14γ = 95.09
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description