1BVT

METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.

Carfi, A.Duee, E.Galleni, M.Frere, J.M.Dideberg, O.

(1998) Acta Crystallogr D Biol Crystallogr 54: 313-323

  • DOI: 10.1107/s0907444997010627
  • Primary Citation of Related Structures:  
    1BVT

  • PubMed Abstract: 
  • Class B beta-lactamases are wide spectrum enzymes which require bivalent metal ions for activity. The structure of the class B zinc-ion-dependent beta-lactamase from Bacillus cereus (BCII) has been refined at 1.85 A resolution using data collected on cryocooled crystals (100 K) ...

    Class B beta-lactamases are wide spectrum enzymes which require bivalent metal ions for activity. The structure of the class B zinc-ion-dependent beta-lactamase from Bacillus cereus (BCII) has been refined at 1.85 A resolution using data collected on cryocooled crystals (100 K). The enzyme from B. cereus has a molecular mass of 24 946 Da and is folded into a beta-sandwich structure with helices on the external faces. The active site is located in a groove running between the two beta-sheets [Carfi et al. (1995). EMBO J. 14, 4914-4921]. The 100 K high-resolution BCII structure shows one fully and one partially occupied zinc sites. The zinc ion in the fully occupied site (the catalytic zinc) is coordinated by three histidines and one water molecule. The second zinc ion is at 3.7 A from the first one and is coordinated by one histidine, one cysteine, one aspartate and one unknown molecule (most likely a carbonate ion). In the B. cereus zinc beta-lactamase the affinity for the second metal-ion is low at the pH of crystallization (Kd = 25 mM, 293 K; [Baldwin et al. (1978). Biochem. J. 175, 441-447] and the dissociation constant of the second zinc ion was thus apparently decreased at the cryogenic temperature. In addition, the structure of the apo enzyme was determined at 2.5 A resolution. The removal of the zinc ion by chelating agents causes small changes in the active-site environment.


    Related Citations: 
    • The 3-D Structure of a Zinc Metallo-Beta-Lactamase from Bacillus Cereus Reveals a New Type of Protein Fold
      Carfi, A., Pares, S., Duee, E., Galleni, M., Duez, C., Frere, J.M., Dideberg, O.
      (1995) EMBO J 14: 4914

    Organizational Affiliation

    LCM, Institut de Biologie Structurale Jean-Pierre Ebel (CEA-CNRS), Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BETA-LACTAMASE)A227Bacillus cereusMutation(s): 0 
Gene Names: blm
EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus)
Explore P04190 
Go to UniProtKB:  P04190
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
C [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53α = 90
b = 61.35β = 92.93
c = 69.45γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Advisory, Data collection
  • Version 1.4: 2018-04-11
    Changes: Data collection