3L6N

Crystal structure of metallo-beta-lactamase IND-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of metallo-beta-lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution

Yamaguchi, Y.Takashio, N.Wachino, J.-I.Yamagata, Y.Arakawa, Y.Matsuda, K.Kurosaki, H.

(2010) J.Biochem. 147: 905-915

  • DOI: 10.1093/jb/mvq029

  • PubMed Abstract: 
  • The X-ray crystal structure of metallo-beta-lactamase from Chryseobacterium indologenes IND-7 was determined at a resolution of 1.65 A. The overall structure adopted a four-layered alphabeta/betaalpha sandwich structure with a dinuclear zinc(II) acti ...

    The X-ray crystal structure of metallo-beta-lactamase from Chryseobacterium indologenes IND-7 was determined at a resolution of 1.65 A. The overall structure adopted a four-layered alphabeta/betaalpha sandwich structure with a dinuclear zinc(II) active site, in which the zinc(II) ions were denoted as Zn1 and Zn2. The overall structure of IND-7 is analogous to those of subclass B1 metallo-beta-lactamases, as determined by X-ray crystallography. A significant structural difference, however, was observed in the dinuclear zinc(II) active site: the coordination geometry around Zn1 changed from tetrahedral, found in other subclass B1 metallo-beta-lactamases, to distorted trigonal bipyramidal, whereas that of Zn2 changed from trigonal bipyramidal to tetrahedral. Arg121(101), which is located in the vicinity of the dinuclear zinc(II) active site, may affect the binding affinity of Zn2 due to an electronic repulsion between the zinc(II) ion(s) and a positively charged guanidyl group of Arg121(101). Moreover, the hydrogen-bonding interaction of Arg121 with Ser71(53), which is conserved in IND-1, IND-3 and IND-5-IND-7, appeared to have important consequences for the binding affinity of Zn2 in conjunction with the above electrostatic effect.


    Organizational Affiliation

    Environmental Safety Center, Kumamoto University, 39-1 Kurokami 2-Chome, Kumamoto 860-8555, Japan. yyamagu@gpo.kumamoto-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
metallo-beta-lactamase
A
219Chryseobacterium indologenesMutation(s): 0 
Gene Names: blaIND-7
Find proteins for A4GRB2 (Chryseobacterium indologenes)
Go to UniProtKB:  A4GRB2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.599α = 90.00
b = 74.313β = 99.38
c = 47.374γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
AMoREphasing
HKL-2000data scaling
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references