3WS2

N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-1C)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure of a highly acidic beta-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site

Arai, S., Yonezawa, Y., Okazaki, N., Matsumoto, F., Shibazaki, C., Shimizu, R., Yamada, M., Adachi, M., Tamada, T., Kawamoto, M., Tokunaga, H., Ishibashi, M., Blaber, M., Tokunaga, M., Kuroki, R.

(2015) Acta Crystallogr D Biol Crystallogr 71: 541-554

  • DOI: 10.1107/S1399004714027734
  • Primary Citation of Related Structures:  
    3WRT, 3WRZ, 3WS0, 3WS1, 3WS2, 3WS4, 3WS5

  • PubMed Abstract: 

    • Environmentally friendly absorbents are needed for Sr(2+) and Cs(+), as the removal of the radioactive Sr(2+) and Cs(+) that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs(+) or Sr(2+) ...

    Environmentally friendly absorbents are needed for Sr(2+) and Cs(+), as the removal of the radioactive Sr(2+) and Cs(+) that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs(+) or Sr(2+). The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P31 using X-ray crystallography. Moreover, the locations of bound Sr(2+) and Cs(+) ions were identified by anomalous X-ray diffraction. The location of one Cs(+)-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na(+) (90 mM Na(+)/10 mM Cs(+)). From an activity assay using isothermal titration calorimetry, the bound Sr(2+) and Cs(+) ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs(+)-binding site provides important information that is useful for the design of artificial Cs(+)-binding sites that may be useful in the bioremediation of radioactive isotopes.

    Organizational Affiliation: 

    Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA, B, C367Chromohalobacter sp. 560Mutation(s): 2 
Gene Names: bla
EC: 3.5.2.6
UniProt
Find proteins for Q76LX5 (Chromohalobacter sp. 560)
Explore Q76LX5 
Go to UniProtKB:  Q76LX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76LX5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.308α = 90
b = 115.308β = 90
c = 67.475γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references