4FZO | pdb_00004fzo

Crystal Structure of the apo-form uranyl binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.176 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.160 (Depositor) 
  • R-Value Observed: 
    0.160 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FZO

This is version 1.2 of the entry. See complete history

Literature

A protein engineered to bind uranyl selectively and with femtomolar affinity.

Zhou, L.Bosscher, M.Zhang, C.Ozcubukcu, S.Zhang, L.Zhang, W.Li, C.J.Liu, J.Jensen, M.P.Lai, L.He, C.

(2014) Nat Chem 6: 236-241

  • DOI: https://doi.org/10.1038/nchem.1856
  • Primary Citation Related Structures: 
    4FZO, 4FZP

  • PubMed Abstract: 

    Uranyl (UO2(2+)), the predominant aerobic form of uranium, is present in the ocean at a concentration of ~3.2 parts per 10(9) (13.7 nM); however, the successful enrichment of uranyl from this vast resource has been limited by the high concentrations of metal ions of similar size and charge, which makes it difficult to design a binding motif that is selective for uranyl. Here we report the design and rational development of a uranyl-binding protein using a computational screening process in the initial search for potential uranyl-binding sites. The engineered protein is thermally stable and offers very high affinity and selectivity for uranyl with a Kd of 7.4 femtomolar (fM) and >10,000-fold selectivity over other metal ions. We also demonstrated that the uranyl-binding protein can repeatedly sequester 30-60% of the uranyl in synthetic sea water. The chemical strategy employed here may be applied to engineer other selective metal-binding proteins for biotechnology and remediation applications.


  • Organizational Affiliation
    • 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA [2].

Macromolecule Content 

  • Total Structure Weight: 19.09 kDa 
  • Atom Count: 1,547 
  • Modeled Residue Count: 162 
  • Deposited Residue Count: 164 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
uranyl binding protein
A, B
82Methanothermobacter thermautotrophicus str. Delta HMutation(s): 4 
Gene Names: MTH_1690
UniProt
Find proteins for O27725 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O27725 
Go to UniProtKB:  O27725
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO27725
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.176 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.160 (Depositor) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.256α = 90
b = 47.034β = 90
c = 65.443γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references