3KNR

Bacillus cereus metallo-beta-lactamase Cys221Asp mutant, 1 mM Zn(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Metallo-beta-lactamases withstand low Zn(II) conditions by tuning metal-ligand interactions.

Gonzalez, J.M.Meini, M.R.Tomatis, P.E.Medrano Martin, F.J.Cricco, J.A.Vila, A.J.

(2012) Nat Chem Biol 8: 698-700

  • DOI: https://doi.org/10.1038/nchembio.1005
  • Primary Citation of Related Structures:  
    3KNR, 3KNS

  • PubMed Abstract: 

    A number of multiresistant bacterial pathogens inactivate antibiotics by producing Zn(II)-dependent β-lactamases. We show that metal uptake leading to an active dinuclear enzyme in the periplasmic space of Gram-negative bacteria is ensured by a cysteine residue, an unusual metal ligand in oxidizing environments. Kinetic, structural and affinity data show that such Zn(II)-cysteine interaction is an adaptive trait that tunes the metal binding affinity, thus enabling antibiotic resistance at restrictive Zn(II) concentrations.


  • Organizational Affiliation

    Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase 2
A, B, C, D
227Bacillus cereusMutation(s): 1 
Gene Names: blm
EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus)
Explore P04190 
Go to UniProtKB:  P04190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04190
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
N [auth C],
O [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
P [auth C],
Q [auth D],
S [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth C]
M [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth C],
M [auth C],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
H [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.143α = 90
b = 94.364β = 120.11
c = 79.898γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-20
    Changes: Database references
  • Version 1.3: 2012-09-05
    Changes: Database references
  • Version 1.4: 2013-06-19
    Changes: Database references
  • Version 1.5: 2017-11-01
    Changes: Refinement description
  • Version 1.6: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.7: 2024-02-21
    Changes: Data collection