3WS4

N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-2A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 

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.,Sect.D 71: 541-554

  • DOI: 10.1107/S1399004714027734
  • Primary Citation of Related Structures:  

  • 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 kno ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C
367Chromohalobacter sp. 560Mutation(s): 2 
Gene Names: bla
EC: 3.5.2.6
Find proteins for Q76LX5 (Chromohalobacter sp. 560)
Go to UniProtKB:  Q76LX5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
A, B, C
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 115.019α = 90.00
b = 115.019β = 90.00
c = 67.800γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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